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Vanderstichele T, Burnham KL, de Klein N, Tardaguila M, Howell B, Walter K, Kundu K, Koeppel J, Lee W, Tokolyi A, Persyn E, Nath AP, Marten J, Petrovski S, Roberts DJ, Di Angelantonio E, Danesh J, Berton A, Platt A, Butterworth AS, Soranzo N, Parts L, Inouye M, Paul DS, Davenport EE. Misexpression of inactive genes in whole blood is associated with nearby rare structural variants. Am J Hum Genet 2024; 111:1524-1543. [PMID: 39053458 PMCID: PMC11339615 DOI: 10.1016/j.ajhg.2024.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024] Open
Abstract
Gene misexpression is the aberrant transcription of a gene in a context where it is usually inactive. Despite its known pathological consequences in specific rare diseases, we have a limited understanding of its wider prevalence and mechanisms in humans. To address this, we analyzed gene misexpression in 4,568 whole-blood bulk RNA sequencing samples from INTERVAL study blood donors. We found that while individual misexpression events occur rarely, in aggregate they were found in almost all samples and a third of inactive protein-coding genes. Using 2,821 paired whole-genome and RNA sequencing samples, we identified that misexpression events are enriched in cis for rare structural variants. We established putative mechanisms through which a subset of SVs lead to gene misexpression, including transcriptional readthrough, transcript fusions, and gene inversion. Overall, we develop misexpression as a type of transcriptomic outlier analysis and extend our understanding of the variety of mechanisms by which genetic variants can influence gene expression.
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Affiliation(s)
| | - Katie L Burnham
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Niek de Klein
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Brittany Howell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Klaudia Walter
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Kousik Kundu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Puddicombe Way, Cambridge, UK
| | - Jonas Koeppel
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Wanseon Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Alex Tokolyi
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Elodie Persyn
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK; Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Artika P Nath
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Jonathan Marten
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK; Department of Medicine, University of Melbourne, Austin Health, Melbourne, VIC, Australia
| | - David J Roberts
- Radcliffe Department of Medicine, John Radcliffe Hospital, Oxford, UK; Clinical Services, NHS Blood and Transplant, Oxford Centre, John Radcliffe Hospital, Oxford, UK
| | - Emanuele Di Angelantonio
- Human Technopole, Fondazione Human Technopole, Milan, Italy; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK; National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - John Danesh
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK; National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Alix Berton
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Molndal, Sweden
| | - Adam Platt
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK; National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Nicole Soranzo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; Human Technopole, Fondazione Human Technopole, Milan, Italy; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Puddicombe Way, Cambridge, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK; National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
| | - Leopold Parts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Michael Inouye
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK; Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Dirk S Paul
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK; Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
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Verkade HJ, Felzen A, Keitel V, Thompson R, Gonzales E, Strnad P, Kamath B, van Mil S. EASL Clinical Practice Guidelines on genetic cholestatic liver diseases. J Hepatol 2024; 81:303-325. [PMID: 38851996 DOI: 10.1016/j.jhep.2024.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 06/10/2024]
Abstract
Genetic cholestatic liver diseases are caused by (often rare) mutations in a multitude of different genes. While these diseases differ in pathobiology, clinical presentation and prognosis, they do have several commonalities due to their cholestatic nature. These Clinical Practice Guidelines (CPGs) offer a general approach to genetic testing and management of cholestatic pruritus, while exploring diagnostic and treatment approaches for a subset of genetic cholestatic liver diseases in depth. An expert panel appointed by the European Association for the Study of the Liver has created recommendations regarding diagnosis and treatment, based on the best evidence currently available in the fields of paediatric and adult hepatology, as well as genetics. The management of these diseases generally takes place in a tertiary referral centre, in order to provide up-to-date approaches and expertise. These CPGs are intended to support hepatologists (for paediatric and adult patients), residents and other healthcare professionals involved in the management of these patients with concrete recommendations based on currently available evidence or, if not available, on expert opinion.
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Rentzsch P, Kollotzek A, Mohammadi P, Lappalainen T. Recalibrating differential gene expression by genetic dosage variance prioritizes functionally relevant genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.10.588830. [PMID: 38645217 PMCID: PMC11030425 DOI: 10.1101/2024.04.10.588830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Differential expression (DE) analysis is a widely used method for identifying genes that are functionally relevant for an observed phenotype or biological response. However, typical DE analysis includes selection of genes based on a threshold of fold change in expression under the implicit assumption that all genes are equally sensitive to dosage changes of their transcripts. This tends to favor highly variable genes over more constrained genes where even small changes in expression may be biologically relevant. To address this limitation, we have developed a method to recalibrate each gene's differential expression fold change based on genetic expression variance observed in the human population. The newly established metric ranks statistically differentially expressed genes not by nominal change of expression, but by relative change in comparison to natural dosage variation for each gene. We apply our method to RNA sequencing datasets from rare disease and in-vitro stimulus response experiments. Compared to the standard approach, our method adjusts the bias in discovery towards highly variable genes, and enriches for pathways and biological processes related to metabolic and regulatory activity, indicating a prioritization of functionally relevant driver genes. With that, our method provides a novel view on DE and contributes towards bridging the existing gap between statistical and biological significance. We believe that this approach will simplify the identification of disease causing genes and enhance the discovery of therapeutic targets.
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Affiliation(s)
- Philipp Rentzsch
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden
| | - Aaron Kollotzek
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden
| | - Pejman Mohammadi
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA; Department of Genome Science, University of Washington, Seattle, WA, USA
| | - Tuuli Lappalainen
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden
- New York Genome Center, New York, NY, USA
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Liu Z, Huang YF. Deep multiple-instance learning accurately predicts gene haploinsufficiency and deletion pathogenicity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555384. [PMID: 37693607 PMCID: PMC10491176 DOI: 10.1101/2023.08.29.555384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Copy number losses (deletions) are a major contributor to the etiology of severe genetic disorders. Although haploinsufficient genes play a critical role in deletion pathogenicity, current methods for deletion pathogenicity prediction fail to integrate multiple lines of evidence for haploinsufficiency at the gene level, limiting their power to pinpoint deleterious deletions associated with genetic disorders. Here we introduce DosaCNV, a deep multiple-instance learning framework that, for the first time, models deletion pathogenicity jointly with gene haploinsufficiency. By integrating over 30 gene-level features potentially predictive of haploinsufficiency, DosaCNV shows unmatched performance in prioritizing pathogenic deletions associated with a broad spectrum of genetic disorders. Furthermore, DosaCNV outperforms existing methods in predicting gene haploinsufficiency even though it is not trained on known haploinsufficient genes. Finally, DosaCNV leverages a state-of-the-art technique to quantify the contributions of individual gene-level features to haploinsufficiency, allowing for human-understandable explanations of model predictions. Altogether, DosaCNV is a powerful computational tool for both fundamental and translational research.
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Affiliation(s)
- Zhihan Liu
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Molecular, Cellular, and Integrative Biosciences Program, Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Yi-Fei Huang
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
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LaPolice TM, Huang YF. An unsupervised deep learning framework for predicting human essential genes from population and functional genomic data. BMC Bioinformatics 2023; 24:347. [PMID: 37723435 PMCID: PMC10506225 DOI: 10.1186/s12859-023-05481-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 09/13/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND The ability to accurately predict essential genes intolerant to loss-of-function (LOF) mutations can dramatically improve the identification of disease-associated genes. Recently, there have been numerous computational methods developed to predict human essential genes from population genomic data. While the existing methods are highly predictive of essential genes of long length, they have limited power in pinpointing short essential genes due to the sparsity of polymorphisms in the human genome. RESULTS Motivated by the premise that population and functional genomic data may provide complementary evidence for gene essentiality, here we present an evolution-based deep learning model, DeepLOF, to predict essential genes in an unsupervised manner. Unlike previous population genetic methods, DeepLOF utilizes a novel deep learning framework to integrate both population and functional genomic data, allowing us to pinpoint short essential genes that can hardly be predicted from population genomic data alone. Compared with previous methods, DeepLOF shows unmatched performance in predicting ClinGen haploinsufficient genes, mouse essential genes, and essential genes in human cell lines. Notably, at a false positive rate of 5%, DeepLOF detects 50% more ClinGen haploinsufficient genes than previous methods. Furthermore, DeepLOF discovers 109 novel essential genes that are too short to be identified by previous methods. CONCLUSION The predictive power of DeepLOF shows that it is a compelling computational method to aid in the discovery of essential genes.
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Affiliation(s)
- Troy M LaPolice
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.
- Bioinformatics and Genomics Graduate Program, Pennsylvania State University, University Park, PA, 16802, USA.
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
| | - Yi-Fei Huang
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
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Liu X, Xu W, Leng F, Zhang P, Guo R, Zhang Y, Hao C, Ni X, Li W. NeuroCNVscore: a tissue-specific framework to prioritise the pathogenicity of CNVs in neurodevelopmental disorders. BMJ Paediatr Open 2023; 7:e001966. [PMID: 37407247 DOI: 10.1136/bmjpo-2023-001966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/15/2023] [Indexed: 07/07/2023] Open
Abstract
BACKGROUND Neurodevelopmental disorders (NDDs) are associated with altered development of the brain especially in childhood. Copy number variants (CNVs) play a crucial role in the genetic aetiology of NDDs by disturbing gene expression directly at linear sequence or remotely at three-dimensional genome level in a tissue-specific manner. Despite the substantial increase in NDD studies employing whole-genome sequencing, there is no specific tool for prioritising the pathogenicity of CNVs in the context of NDDs. METHODS Using an XGBoost classifier, we integrated 189 features that represent genomic sequences, gene information and functional/genomic segments for evaluating genome-wide CNVs in a neuro/brain-specific manner, to develop a new tool, neuroCNVscore. We used Human Phenotype Ontology to construct an independent NDD-related set. RESULTS Our neuroCNVscore framework (https://github.com/lxsbch/neuroCNVscore) achieved high predictive performance (precision recall=0.82; area under curve=0.85) and outperformed an existing reference method SVScore. Notably, the predicted pathogenic CNVs showed enrichment in known genes associated with autism. CONCLUSIONS NeuroCNVscore prioritises functional, deleterious and pathogenic CNVs in NDDs at whole genome-wide level, which is important for genetic studies and clinical genomic screening of NDDs as well as for providing novel biological insights into NDDs.
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Affiliation(s)
- Xuanshi Liu
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- Genetics and Birth Defects Control Centre, National Centre for Children's Health, Beijing, China
| | - Wenjian Xu
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- Genetics and Birth Defects Control Centre, National Centre for Children's Health, Beijing, China
| | - Fei Leng
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- Genetics and Birth Defects Control Centre, National Centre for Children's Health, Beijing, China
| | - Peng Zhang
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- Genetics and Birth Defects Control Centre, National Centre for Children's Health, Beijing, China
| | - Ruolan Guo
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- Genetics and Birth Defects Control Centre, National Centre for Children's Health, Beijing, China
| | - Yue Zhang
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- Genetics and Birth Defects Control Centre, National Centre for Children's Health, Beijing, China
| | - Chanjuan Hao
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- Genetics and Birth Defects Control Centre, National Centre for Children's Health, Beijing, China
| | - Xin Ni
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- National Centre for Children's Health, Beijing, China
| | - Wei Li
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- Genetics and Birth Defects Control Centre, National Centre for Children's Health, Beijing, China
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Lv K, Chen D, Xiong D, Tang H, Ou T, Kan L, Zhang X. dbCNV: deleteriousness-based model to predict pathogenicity of copy number variations. BMC Genomics 2023; 24:131. [PMID: 36941551 PMCID: PMC10029177 DOI: 10.1186/s12864-023-09225-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/06/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Copy number variation (CNV) is a type of structural variation, which is a gain or loss event with abnormal changes in copy number. Methods to predict the pathogenicity of CNVs are required to realize the relationship between these variants and clinical phenotypes. ClassifyCNV, X-CNV, StrVCTVRE, etc. have been trained to predict the pathogenicity of CNVs, but few studies have been reported based on the deleterious significance of features. RESULTS From single nucleotide polymorphism (SNP), gene and region dimensions, we collected 79 informative features that quantitatively describe the characteristics of CNV, such as CNV length, the number of protein genes, the number of three prime untranslated region. Then, according to the deleterious significance, we formulated quantitative methods for features, which fall into two categories: the first is variable type, including maximum, minimum and mean; the second is attribute type, which is measured by numerical sum. We used Gradient Boosted Trees (GBT) algorithm to construct dbCNV, which can be used to predict pathogenicity for five-tier classification and binary classification of CNVs. We demonstrated that the distribution of most feature values was consistent with the deleterious significance. The five-tier classification model accuracy for 0.85 and 0.79 in loss and gain CNVs, which proved that it has high discrimination power in predicting the pathogenicity of five-tier classification CNVs. The binary model achieved area under curve (AUC) values of 0.96 and 0.81 in the validation set, respectively, in gain and loss CNVs. CONCLUSION The performance of the dbCNV suggest that functional deleteriousness-based model of CNV is a promising approach to support the classification prediction and to further understand the pathogenic mechanism.
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Affiliation(s)
- Kangqi Lv
- Xinxiang Medical University, 453003, Xinxiang, China
- Medical Laboratory of the Third Affiliated Hospital of Shenzhen University, No. 47 of Youyi Road, 518001, Shenzhen City, Guangdong Province, China
| | - Dayang Chen
- Medical Laboratory of the Third Affiliated Hospital of Shenzhen University, No. 47 of Youyi Road, 518001, Shenzhen City, Guangdong Province, China
| | - Dan Xiong
- Medical Laboratory of the Third Affiliated Hospital of Shenzhen University, No. 47 of Youyi Road, 518001, Shenzhen City, Guangdong Province, China
| | - Huamei Tang
- Medical Laboratory of the Third Affiliated Hospital of Shenzhen University, No. 47 of Youyi Road, 518001, Shenzhen City, Guangdong Province, China
| | - Tong Ou
- Medical Laboratory of the Third Affiliated Hospital of Shenzhen University, No. 47 of Youyi Road, 518001, Shenzhen City, Guangdong Province, China
| | - Lijuan Kan
- Medical Laboratory of the Third Affiliated Hospital of Shenzhen University, No. 47 of Youyi Road, 518001, Shenzhen City, Guangdong Province, China.
| | - Xiuming Zhang
- Xinxiang Medical University, 453003, Xinxiang, China
- Medical Laboratory of the Third Affiliated Hospital of Shenzhen University, No. 47 of Youyi Road, 518001, Shenzhen City, Guangdong Province, China
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Ambrosini C, Destefanis E, Kheir E, Broso F, Alessandrini F, Longhi S, Battisti N, Pesce I, Dassi E, Petris G, Cereseto A, Quattrone A. Translational enhancement by base editing of the Kozak sequence rescues haploinsufficiency. Nucleic Acids Res 2022; 50:10756-10771. [PMID: 36165847 PMCID: PMC9561285 DOI: 10.1093/nar/gkac799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 09/01/2022] [Accepted: 09/22/2022] [Indexed: 11/28/2022] Open
Abstract
A variety of single-gene human diseases are caused by haploinsufficiency, a genetic condition by which mutational inactivation of one allele leads to reduced protein levels and functional impairment. Translational enhancement of the spare allele could exert a therapeutic effect. Here we developed BOOST, a novel gene-editing approach to rescue haploinsufficiency loci by the change of specific single nucleotides in the Kozak sequence, which controls translation by regulating start codon recognition. We evaluated for translational strength 230 Kozak sequences of annotated human haploinsufficient genes and 4621 derived variants, which can be installed by base editing, by a high-throughput reporter assay. Of these variants, 149 increased the translation of 47 Kozak sequences, demonstrating that a substantial proportion of haploinsufficient genes are controlled by suboptimal Kozak sequences. Validation of 18 variants for 8 genes produced an average enhancement in an expression window compatible with the rescue of the genetic imbalance. Base editing of the NCF1 gene, whose monoallelic loss causes chronic granulomatous disease, resulted in the desired increase of NCF1 (p47phox) protein levels in a relevant cell model. We propose BOOST as a fine-tuned approach to modulate translation, applicable to the correction of dozens of haploinsufficient monogenic disorders independently of the causing mutation.
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Affiliation(s)
- Chiara Ambrosini
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Eliana Destefanis
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Eyemen Kheir
- Laboratory of Molecular Virology, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Francesca Broso
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Federica Alessandrini
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Sara Longhi
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Nicolò Battisti
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Isabella Pesce
- Cell Analysis and Separation Core Facility, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Erik Dassi
- Laboratory of RNA Regulatory Networks, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Gianluca Petris
- Medical Research Council Laboratory of Molecular Biology (MRC LMB), Cambridge CB2 0QH, UK
| | - Anna Cereseto
- Laboratory of Molecular Virology, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
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Pathological variants in genes associated with disorders of sex development and central causes of hypogonadism in a whole-genome reference panel of 8380 Japanese individuals. Hum Genome Var 2022; 9:34. [PMID: 36171209 PMCID: PMC9519586 DOI: 10.1038/s41439-022-00213-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 08/23/2022] [Accepted: 08/23/2022] [Indexed: 01/15/2023] Open
Abstract
Disorders of sex development (DSD) comprises a congenital condition in which chromosomal, gonadal, or anatomical sex development is atypical. In this study, we screened for pathogenic variants in 32 genes associated with DSDs and central causes of hypogonadism (CHG) in a whole-genome reference panel including 8380 Japanese individuals constructed by Tohoku Medical Megabank Organization. Candidate pathogenic (P) or likely pathogenic (LP) variants were extracted from the ClinVar, InterVar, and Human Gene Mutation databases. Ninety-one candidate pathological variants were found in 25 genes; 28 novel candidate variants were identified. Nearly 1 in 40 (either ClinVar or InterVar P or LP) to 157 (both ClinVar and InterVar P or LP) individuals were found to be carriers of recessive DSD and CHG alleles. In these data, genes implicated in gonadal dysfunction did not show loss-of-function variants, with a relatively high tendency of intolerance for haploinsufficiency based on pLI and Episcore, both of which can be used for estimating haploinsufficiency. We report the types and frequencies of causative variants for DSD and CHG in the general Japanese population. This study furthers our understanding of the genetic causes and helps to refine genetic counseling of DSD and CHG.
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Li K, Luo T, Zhu Y, Huang Y, Wang A, Zhang D, Dong L, Wang Y, Wang R, Tang D, Yu Z, Shen Q, Lv M, Ling Z, Fang Z, Yuan J, Li B, Xia K, He X, Li J, Zhao G. Performance evaluation of differential splicing analysis methods and splicing analytics platform construction. Nucleic Acids Res 2022; 50:9115-9126. [PMID: 35993808 PMCID: PMC9458456 DOI: 10.1093/nar/gkac686] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 07/01/2022] [Accepted: 08/01/2022] [Indexed: 12/24/2022] Open
Abstract
A proportion of previously defined benign variants or variants of uncertain significance in humans, which are challenging to identify, may induce an abnormal splicing process. An increasing number of methods have been developed to predict splicing variants, but their performance has not been completely evaluated using independent benchmarks. Here, we manually sourced ∼50 000 positive/negative splicing variants from > 8000 studies and selected the independent splicing variants to evaluate the performance of prediction methods. These methods showed different performances in recognizing splicing variants in donor and acceptor regions, reminiscent of different weight coefficient applications to predict novel splicing variants. Of these methods, 66.67% exhibited higher specificities than sensitivities, suggesting that more moderate cut-off values are necessary to distinguish splicing variants. Moreover, the high correlation and consistent prediction ratio validated the feasibility of integration of the splicing prediction method in identifying splicing variants. We developed a splicing analytics platform called SPCards, which curates splicing variants from publications and predicts splicing scores of variants in genomes. SPCards also offers variant-level and gene-level annotation information, including allele frequency, non-synonymous prediction and comprehensive functional information. SPCards is suitable for high-throughput genetic identification of splicing variants, particularly those located in non-canonical splicing regions.
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Affiliation(s)
| | | | - Yan Zhu
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yuanfeng Huang
- Bioinformatics Center & National Clinical Research Centre for Geriatric Disorders & Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - An Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Di Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Lijie Dong
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yujian Wang
- Bioinformatics Center & National Clinical Research Centre for Geriatric Disorders & Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Rui Wang
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Dongdong Tang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Zhen Yu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Qunshan Shen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Mingrong Lv
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Zhengbao Ling
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Zhenghuan Fang
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jing Yuan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Bin Li
- Bioinformatics Center & National Clinical Research Centre for Geriatric Disorders & Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Kun Xia
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China,Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Xiaojin He
- Correspondence may also be addressed to Xiaojin He. Tel: +86 731 8975 2406; Fax: +86 731 8432 7332;
| | - Jinchen Li
- To whom correspondence should be addressed. Tel: +86 731 8975 2406; Fax: +86 731 8432 7332;
| | - Guihu Zhao
- Correspondence may also be addressed to Guihu Zhao. Tel: +86 731 8975 2406; Fax: +86 731 8432 7332;
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11
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Lin X, Liu Y, Liu S, Zhu X, Wu L, Zhu Y, Zhao D, Xu X, Chemparathy A, Wang H, Cao Y, Nakamura M, Noordermeer JN, La Russa M, Wong WH, Zhao K, Qi LS. Nested epistasis enhancer networks for robust genome regulation. Science 2022; 377:1077-1085. [PMID: 35951677 DOI: 10.1126/science.abk3512] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mammalian genomes possess multiple enhancers spanning an ultralong distance (>megabases) to modulate important genes, yet it is unclear how these enhancers coordinate to achieve this task. Here, we combine multiplexed CRISPRi screening with machine learning to define quantitative enhancer-enhancer interactions. We find that the ultralong distance enhancer network possesses a nested multi-layer architecture that confers functional robustness of gene expression. Experimental characterization reveals that enhancer epistasis is maintained by three-dimensional chromosomal interactions and BRD4 condensation. Machine learning prediction of synergistic enhancers provides an effective strategy to identify non-coding variant pairs associated with pathogenic genes in diseases beyond Genome-Wide Association Studies (GWAS) analysis. Our work unveils nested epistasis enhancer networks, which can better explain enhancer functions within cells and in diseases.
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Affiliation(s)
- Xueqiu Lin
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Yanxia Liu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Shuai Liu
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute NIH, Bethesda, MD 20892, USA
| | - Xiang Zhu
- Department of Statistics, Stanford University, Stanford, CA 94305, USA.,Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lingling Wu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Yanyu Zhu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Dehua Zhao
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Xiaoshu Xu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Haifeng Wang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Yaqiang Cao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute NIH, Bethesda, MD 20892, USA
| | - Muneaki Nakamura
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Marie La Russa
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Wing Hung Wong
- Department of Statistics, Stanford University, Stanford, CA 94305, USA.,Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute NIH, Bethesda, MD 20892, USA
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,ChEM-H, Stanford University, Stanford, CA 94305, USA.,Chan Zuckerberg BioHub, San Francisco, CA 94158, USA
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12
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Collins RL, Glessner JT, Porcu E, Lepamets M, Brandon R, Lauricella C, Han L, Morley T, Niestroj LM, Ulirsch J, Everett S, Howrigan DP, Boone PM, Fu J, Karczewski KJ, Kellaris G, Lowther C, Lucente D, Mohajeri K, Nõukas M, Nuttle X, Samocha KE, Trinh M, Ullah F, Võsa U, Hurles ME, Aradhya S, Davis EE, Finucane H, Gusella JF, Janze A, Katsanis N, Matyakhina L, Neale BM, Sanders D, Warren S, Hodge JC, Lal D, Ruderfer DM, Meck J, Mägi R, Esko T, Reymond A, Kutalik Z, Hakonarson H, Sunyaev S, Brand H, Talkowski ME. A cross-disorder dosage sensitivity map of the human genome. Cell 2022; 185:3041-3055.e25. [PMID: 35917817 PMCID: PMC9742861 DOI: 10.1016/j.cell.2022.06.036] [Citation(s) in RCA: 130] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/17/2022] [Accepted: 06/20/2022] [Indexed: 02/06/2023]
Abstract
Rare copy-number variants (rCNVs) include deletions and duplications that occur infrequently in the global human population and can confer substantial risk for disease. In this study, we aimed to quantify the properties of haploinsufficiency (i.e., deletion intolerance) and triplosensitivity (i.e., duplication intolerance) throughout the human genome. We harmonized and meta-analyzed rCNVs from nearly one million individuals to construct a genome-wide catalog of dosage sensitivity across 54 disorders, which defined 163 dosage sensitive segments associated with at least one disorder. These segments were typically gene dense and often harbored dominant dosage sensitive driver genes, which we were able to prioritize using statistical fine-mapping. Finally, we designed an ensemble machine-learning model to predict probabilities of dosage sensitivity (pHaplo & pTriplo) for all autosomal genes, which identified 2,987 haploinsufficient and 1,559 triplosensitive genes, including 648 that were uniquely triplosensitive. This dosage sensitivity resource will provide broad utility for human disease research and clinical genetics.
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Affiliation(s)
- Ryan L Collins
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - Joseph T Glessner
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Division of Human Genetics, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Eleonora Porcu
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Maarja Lepamets
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia; Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia
| | | | | | - Lide Han
- Division of Genetic Medicine, Department of Medicine, and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Theodore Morley
- Division of Genetic Medicine, Department of Medicine, and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Jacob Ulirsch
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Selin Everett
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Daniel P Howrigan
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Philip M Boone
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Jack Fu
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Konrad J Karczewski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Georgios Kellaris
- Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Lurie Children's Hospital, Chicago, IL 60611, USA; Departments of Pediatrics and Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Chelsea Lowther
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Diane Lucente
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kiana Mohajeri
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Margit Nõukas
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia; Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia
| | - Xander Nuttle
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Kaitlin E Samocha
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10, UK
| | - Mi Trinh
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10, UK
| | - Farid Ullah
- Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Lurie Children's Hospital, Chicago, IL 60611, USA; Departments of Pediatrics and Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Urmo Võsa
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | | | | | - Matthew E Hurles
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10, UK
| | | | - Erica E Davis
- Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Lurie Children's Hospital, Chicago, IL 60611, USA; Departments of Pediatrics and Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Hilary Finucane
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - James F Gusella
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | | | - Nicholas Katsanis
- Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Lurie Children's Hospital, Chicago, IL 60611, USA; Departments of Pediatrics and Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | | | - Benjamin M Neale
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | | | - Jennelle C Hodge
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Dennis Lal
- Cologne Center for Genomics, University of Cologne, 51149 Cologne, Germany; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Douglas M Ruderfer
- Division of Genetic Medicine, Department of Medicine, and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Center for Precision Medicine, Department of Biomedical Informatics, and Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Tõnu Esko
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Zoltán Kutalik
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Center for Primary Care and Public Health, University of Lausanne, 1015 Lausanne, Switzerland; Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Hakon Hakonarson
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Division of Human Genetics, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Shamil Sunyaev
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA.
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
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13
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Huang S, Zhao G, Wu J, Li K, Wang Q, Fu Y, Zhang H, Bi Q, Li X, Wang W, Guo C, Zhang D, Wu L, Li X, Xu H, Han M, Wang X, Lei C, Qiu X, Li Y, Li J, Dai P, Yuan Y. Gene4HL: An Integrated Genetic Database for Hearing Loss. Front Genet 2021; 12:773009. [PMID: 34733322 PMCID: PMC8558372 DOI: 10.3389/fgene.2021.773009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 09/28/2021] [Indexed: 11/18/2022] Open
Abstract
Hearing loss (HL) is one of the most common disabilities in the world. In industrialized countries, HL occurs in 1–2/1,000 newborns, and approximately 60% of HL is caused by genetic factors. Next generation sequencing (NGS) has been widely used to identify many candidate genes and variants in patients with HL, but the data are scattered in multitudinous studies. It is a challenge for scientists, clinicians, and biologists to easily obtain and analyze HL genes and variant data from these studies. Thus, we developed a one-stop database of HL-related genes and variants, Gene4HL (http://www.genemed.tech/gene4hl/), making it easy to catalog, search, browse and analyze the genetic data. Gene4HL integrates the detailed genetic and clinical data of 326 HL-related genes from 1,608 published studies, along with 62 popular genetic data sources to provide comprehensive knowledge of candidate genes and variants associated with HL. Additionally, Gene4HL supports the users to analyze their own genetic engineering network data, performs comprehensive annotation, and prioritizes candidate genes and variations using custom parameters. Thus, Gene4HL can help users explain the function of HL genes and the clinical significance of variants by correlating the genotypes and phenotypes in humans.
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Affiliation(s)
- Shasha Huang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China.,Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Jie Wu
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Kuokuo Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China.,Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Qiuquan Wang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Ying Fu
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Honglei Zhang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Qingling Bi
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Xiaohong Li
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Weiqian Wang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Chang Guo
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Dejun Zhang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Lihua Wu
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Xiaoge Li
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Huiyan Xu
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Mingyu Han
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Xin Wang
- Angen Gene Medicine Technology Co., Ltd., Beijing, China
| | - Chen Lei
- Angen Gene Medicine Technology Co., Ltd., Beijing, China
| | - Xiaofang Qiu
- Angen Gene Medicine Technology Co., Ltd., Beijing, China
| | - Yang Li
- Angen Gene Medicine Technology Co., Ltd., Beijing, China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China.,Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Pu Dai
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Yongyi Yuan
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
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14
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Parrello D, Vlasenok M, Kranz L, Nechaev S. Targeting the Transcriptome Through Globally Acting Components. Front Genet 2021; 12:749850. [PMID: 34603400 PMCID: PMC8481634 DOI: 10.3389/fgene.2021.749850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/02/2021] [Indexed: 11/13/2022] Open
Abstract
Transcription is a step in gene expression that defines the identity of cells and its dysregulation is associated with diseases. With advancing technologies revealing molecular underpinnings of the cell with ever-higher precision, our ability to view the transcriptomes may have surpassed our knowledge of the principles behind their organization. The human RNA polymerase II (Pol II) machinery comprises thousands of components that, in conjunction with epigenetic and other mechanisms, drive specialized programs of development, differentiation, and responses to the environment. Parts of these programs are repurposed in oncogenic transformation. Targeting of cancers is commonly done by inhibiting general or broadly acting components of the cellular machinery. The critical unanswered question is how globally acting or general factors exert cell type specific effects on transcription. One solution, which is discussed here, may be among the events that take place at genes during early Pol II transcription elongation. This essay turns the spotlight on the well-known phenomenon of promoter-proximal Pol II pausing as a step that separates signals that establish pausing genome-wide from those that release the paused Pol II into the gene. Concepts generated in this rapidly developing field will enhance our understanding of basic principles behind transcriptome organization and hopefully translate into better therapies at the bedside.
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Affiliation(s)
- Damien Parrello
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, United States
| | - Maria Vlasenok
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Lincoln Kranz
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, United States
| | - Sergei Nechaev
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, United States
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15
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Zhang L, Shi J, Ouyang J, Zhang R, Tao Y, Yuan D, Lv C, Wang R, Ning B, Roberts R, Tong W, Liu Z, Shi T. X-CNV: genome-wide prediction of the pathogenicity of copy number variations. Genome Med 2021; 13:132. [PMID: 34407882 PMCID: PMC8375180 DOI: 10.1186/s13073-021-00945-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 07/30/2021] [Indexed: 01/04/2023] Open
Abstract
Background Gene copy number variations (CNVs) contribute to genetic diversity and disease prevalence across populations. Substantial efforts have been made to decipher the relationship between CNVs and pathogenesis but with limited success. Results We have developed a novel computational framework X-CNV (www.unimd.org/XCNV), to predict the pathogenicity of CNVs by integrating more than 30 informative features such as allele frequency (AF), CNV length, CNV type, and some deleterious scores. Notably, over 14 million CNVs across various ethnic groups, covering nearly 93% of the human genome, were unified to calculate the AF. X-CNV, which yielded area under curve (AUC) values of 0.96 and 0.94 in training and validation sets, was demonstrated to outperform other available tools in terms of CNV pathogenicity prediction. A meta-voting prediction (MVP) score was developed to quantitively measure the pathogenic effect, which is based on the probabilistic value generated from the XGBoost algorithm. The proposed MVP score demonstrated a high discriminative power in determining pathogenetic CNVs for inherited traits/diseases in different ethnic groups. Conclusions The ability of the X-CNV framework to quantitatively prioritize functional, deleterious, and disease-causing CNV on a genome-wide basis outperformed current CNV-annotation tools and will have broad utility in population genetics, disease-association studies, and diagnostic screening. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00945-4.
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Affiliation(s)
- Li Zhang
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China.,School of Statistics, Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, East China Normal University, Shanghai, 200062, China
| | - Jingru Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jian Ouyang
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Riquan Zhang
- School of Statistics, Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, East China Normal University, Shanghai, 200062, China
| | - Yiran Tao
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Dongsheng Yuan
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Chengkai Lv
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Ruiyuan Wang
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Baitang Ning
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Ruth Roberts
- ApconiX Ltd, Alderley Park, Alderley Edge, SK10 4TG, UK.,University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Weida Tong
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA.
| | - Zhichao Liu
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA.
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China. .,School of Statistics, Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, East China Normal University, Shanghai, 200062, China. .,Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing, 100083, China.
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16
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Li B, Wang Z, Chen Q, Li K, Wang X, Wang Y, Zeng Q, Han Y, Lu B, Zhao Y, Zhang R, Jiang L, Pan H, Luo T, Zhang Y, Fang Z, Xiao X, Zhou X, Wang R, Zhou L, Wang Y, Yuan Z, Xia L, Guo J, Tang B, Xia K, Zhao G, Li J. GPCards: An integrated database of genotype-phenotype correlations in human genetic diseases. Comput Struct Biotechnol J 2021; 19:1603-1611. [PMID: 33868597 PMCID: PMC8042245 DOI: 10.1016/j.csbj.2021.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/28/2021] [Accepted: 03/10/2021] [Indexed: 01/02/2023] Open
Abstract
The patient-level genotype-phenotype correlations in GPCards accelerated the development of medical genetics. The integrated 62 genomic sources provide comprehensive information for interpreting pathogenicity. Analysis function in GPCards would help users to decipher their data of genotype-phenotype correlations.
Genotype–phenotype correlations are the basis of precision medicine of human genetic diseases. However, it remains a challenge for clinicians and researchers to conveniently access detailed individual-level clinical phenotypic features of patients with various genetic variants. To address this urgent need, we manually searched for genetic studies in PubMed and catalogued 8,309 genetic variants in 1,288 genes from 17,738 patients with detailed clinical phenotypic features from 1,855 publications. Based on genotype–phenotype correlations in this dataset, we developed an user-friendly online database called GPCards (http://genemed.tech/gpcards/), which not only provided the association between genetic diseases and disease genes, but also the prevalence of various clinical phenotypes related to disease genes and the patient-level mapping between these clinical phenotypes and genetic variants. To accelerate the interpretation of genetic variants, we integrated 62 well-known variant-level and gene-level genomic data sources, including functional predictions, allele frequencies in different populations, and disease-related information. Furthermore, GPCards enables automatic analyses of users’ own genetic data, comprehensive annotation, prioritization of candidate functional variants, and identification of genotype–phenotype correlations using custom parameters. In conclusion, GPCards is expected to accelerate the interpretation of genotype–phenotype correlations, subtype classification, and candidate gene prioritisation in human genetic diseases.
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Affiliation(s)
- Bin Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,Mobile Health Ministry of Education - China Mobile Joint Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zheng Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Qian Chen
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Kuokuo Li
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha Hunan 410008, China
| | - Xiaomeng Wang
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha Hunan 410008, China
| | - Yijing Wang
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha Hunan 410008, China
| | - Qian Zeng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Ying Han
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha Hunan 410008, China
| | - Bin Lu
- Department of Pathogen Biology, School of Basic Medical Sciences, Central South University, Changsha, Hunan 410008, China
| | - Yuwen Zhao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Rui Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Li Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Hongxu Pan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Tengfei Luo
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha Hunan 410008, China
| | - Yi Zhang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhenghuan Fang
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha Hunan 410008, China
| | - Xuewen Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xun Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Rui Wang
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha Hunan 410008, China
| | - Lu Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yige Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhenhua Yuan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Lu Xia
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha Hunan 410008, China
| | - Jifeng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Beisha Tang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Kun Xia
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha Hunan 410008, China
| | - Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha Hunan 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
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17
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Yang Y, Li S, Wang Y, Ma Z, Wong KC, Li X. Identification of haploinsufficient genes from epigenomic data using deep forest. Brief Bioinform 2021; 22:6102676. [PMID: 33454736 DOI: 10.1093/bib/bbaa393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 11/29/2020] [Accepted: 12/01/2020] [Indexed: 11/14/2022] Open
Abstract
Haploinsufficiency, wherein a single allele is not enough to maintain normal functions, can lead to many diseases including cancers and neurodevelopmental disorders. Recently, computational methods for identifying haploinsufficiency have been developed. However, most of those computational methods suffer from study bias, experimental noise and instability, resulting in unsatisfactory identification of haploinsufficient genes. To address those challenges, we propose a deep forest model, called HaForest, to identify haploinsufficient genes. The multiscale scanning is proposed to extract local contextual representations from input features under Linear Discriminant Analysis. After that, the cascade forest structure is applied to obtain the concatenated features directly by integrating decision-tree-based forests. Meanwhile, to exploit the complex dependency structure among haploinsufficient genes, the LightGBM library is embedded into HaForest to reveal the highly expressive features. To validate the effectiveness of our method, we compared it to several computational methods and four deep learning algorithms on five epigenomic data sets. The results reveal that HaForest achieves superior performance over the other algorithms, demonstrating its unique and complementary performance in identifying haploinsufficient genes. The standalone tool is available at https://github.com/yangyn533/HaForest.
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Affiliation(s)
- Yuning Yang
- School of Artificial Intelligence, Jilin University and School of Information Science and Technology, Northeast Normal University, China
| | - Shaochuan Li
- School of Information Science and Technology, Northeast Normal University, China
| | - Yunhe Wang
- School of Information Science and Technology, Northeast Normal University, China
| | - Zhiqiang Ma
- School of Information Science and Technology, Northeast Normal University, China
| | | | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, Changchun, Jilin, China
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18
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Wang J, Ahimaz PR, Hashemifar S, Khlevner J, Picoraro JA, Middlesworth W, Elfiky MM, Que J, Shen Y, Chung WK. Novel candidate genes in esophageal atresia/tracheoesophageal fistula identified by exome sequencing. Eur J Hum Genet 2021; 29:122-130. [PMID: 32641753 PMCID: PMC7852873 DOI: 10.1038/s41431-020-0680-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/07/2020] [Accepted: 06/23/2020] [Indexed: 12/24/2022] Open
Abstract
The various malformations of the aerodigestive tract collectively known as esophageal atresia/tracheoesophageal fistula (EA/TEF) constitute a rare group of birth defects of largely unknown etiology. Previous studies have identified a small number of rare genetic variants causing syndromes associated with EA/TEF. We performed a pilot exome sequencing study of 45 unrelated simplex trios (probands and parents) with EA/TEF. Thirteen had isolated and 32 had nonisolated EA/TEF; none had a family history of EA/TEF. We identified de novo variants in protein-coding regions, including 19 missense variants predicted to be deleterious (D-mis) and 3 likely gene-disrupting (LGD) variants. Consistent with previous studies of structural birth defects, there is a trend of increased burden of de novo D-mis in cases (1.57-fold increase over the background mutation rate), and the burden is greater in constrained genes (2.55-fold, p = 0.003). There is a frameshift de novo variant in EFTUD2, a known EA/TEF risk gene involved in mRNA splicing. Strikingly, 15 out of 19 de novo D-mis variants are located in genes that are putative target genes of EFTUD2 or SOX2 (another known EA/TEF gene), much greater than expected by chance (3.34-fold, p value = 7.20e-5). We estimated that 33% of patients can be attributed to de novo deleterious variants in known and novel genes. We identified APC2, AMER3, PCDH1, GTF3C1, POLR2B, RAB3GAP2, and ITSN1 as plausible candidate genes in the etiology of EA/TEF. We conclude that further genomic analysis to identify de novo variants will likely identify previously undescribed genetic causes of EA/TEF.
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Affiliation(s)
- Jiayao Wang
- grid.239585.00000 0001 2285 2675Department of Pediatrics, Columbia University Medical Center, New York, NY USA ,grid.239585.00000 0001 2285 2675Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York, NY USA
| | - Priyanka R. Ahimaz
- grid.239585.00000 0001 2285 2675Department of Pediatrics, Columbia University Medical Center, New York, NY USA
| | - Somaye Hashemifar
- grid.239585.00000 0001 2285 2675Department of Pediatrics, Columbia University Medical Center, New York, NY USA ,grid.239585.00000 0001 2285 2675Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York, NY USA
| | - Julie Khlevner
- grid.239585.00000 0001 2285 2675Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Columbia University Medical Center, New York, NY USA
| | - Joseph A. Picoraro
- grid.239585.00000 0001 2285 2675Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Columbia University Medical Center, New York, NY USA
| | - William Middlesworth
- grid.239585.00000 0001 2285 2675Division of Pediatric Surgery, Department of Surgery, Columbia University Medical Center, New York, NY USA
| | - Mahmoud M. Elfiky
- grid.7776.10000 0004 0639 9286Pediatric Surgery, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Jianwen Que
- grid.239585.00000 0001 2285 2675Department of Medicine, Columbia University Medical Center, New York, NY USA
| | - Yufeng Shen
- grid.239585.00000 0001 2285 2675Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York, NY USA
| | - Wendy K. Chung
- grid.239585.00000 0001 2285 2675Department of Pediatrics, Columbia University Medical Center, New York, NY USA ,grid.239585.00000 0001 2285 2675Department of Medicine, Columbia University Medical Center, New York, NY USA
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19
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Khan P, Siddiqui JA, Maurya SK, Lakshmanan I, Jain M, Ganti AK, Salgia R, Batra SK, Nasser MW. Epigenetic landscape of small cell lung cancer: small image of a giant recalcitrant disease. Semin Cancer Biol 2020; 83:57-76. [PMID: 33220460 PMCID: PMC8218609 DOI: 10.1016/j.semcancer.2020.11.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/12/2022]
Abstract
Small cell lung cancer (SCLC) is a particular subtype of lung cancer with high mortality. Recent advances in understanding SCLC genomics and breakthroughs of immunotherapy have substantially expanded existing knowledge and treatment modalities. However, challenges associated with SCLC remain enigmatic and elusive. Most of the conventional drug discovery approaches targeting altered signaling pathways in SCLC end up in the 'grave-yard of drug discovery', which mandates exploring novel approaches beyond inhibiting cell signaling pathways. Epigenetic modifications have long been documented as the key contributors to the tumorigenesis of almost all types of cancer, including SCLC. The last decade witnessed an exponential increase in our understanding of epigenetic modifications for SCLC. The present review highlights the central role of epigenetic regulations in acquiring neoplastic phenotype, metastasis, aggressiveness, resistance to chemotherapy, and immunotherapeutic approaches of SCLC. Different types of epigenetic modifications (DNA/histone methylation or acetylation) that can serve as predictive biomarkers for prognostication, treatment stratification, neuroendocrine lineage determination, and development of potential SCLC therapies are also discussed. We also review the utility of epigenetic targets/epidrugs in combination with first-line chemotherapy and immunotherapy that are currently under investigation in preclinical and clinical studies. Altogether, the information presents the inclusive landscape of SCLC epigenetics and epidrugs that will help to improve SCLC outcomes.
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Affiliation(s)
- Parvez Khan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Jawed Akhtar Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Shailendra Kumar Maurya
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Imayavaramban Lakshmanan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Maneesh Jain
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Apar Kishor Ganti
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; Division of Oncology-Hematology, Department of Internal Medicine, VA-Nebraska Western Iowa Health Care System, Omaha, NE, 68105, USA; Division of Oncology-Hematology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte 91010, CA, USA
| | - Surinder Kumar Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Mohd Wasim Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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20
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Boukas L, Bjornsson HT, Hansen KD. Promoter CpG Density Predicts Downstream Gene Loss-of-Function Intolerance. Am J Hum Genet 2020; 107:487-498. [PMID: 32800095 PMCID: PMC7477270 DOI: 10.1016/j.ajhg.2020.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/22/2020] [Indexed: 12/26/2022] Open
Abstract
The aggregation and joint analysis of large numbers of exome sequences has recently made it possible to derive estimates of intolerance to loss-of-function (LoF) variation for human genes. Here, we demonstrate strong and widespread coupling between genic LoF intolerance and promoter CpG density across the human genome. Genes downstream of the most CpG-rich promoters (top 10% CpG density) have a 67.2% probability of being highly LoF intolerant, using the LOEUF metric from gnomAD. This is in contrast to 7.4% of genes downstream of the most CpG-poor (bottom 10% CpG density) promoters. Combining promoter CpG density with exonic and promoter conservation explains 33.4% of the variation in LOEUF, and the contribution of CpG density exceeds the individual contributions of exonic and promoter conservation. We leverage this to train a simple and easily interpretable predictive model that outperforms other existing predictors and allows us to classify 1,760 genes-which are currently unascertained in gnomAD-as highly LoF intolerant or not. These predictions have the potential to aid in the interpretation of novel variants in the clinical setting. Moreover, our results reveal that high CpG density is not merely a generic feature of human promoters but is preferentially encountered at the promoters of the most selectively constrained genes, calling into question the prevailing view that CpG islands are not subject to selection.
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Affiliation(s)
- Leandros Boukas
- Human Genetics Training Program, Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA
| | - Hans T Bjornsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA; Department of Pediatrics, Johns Hopkins University School of Medicine, 1800 Orleans Street, Baltimore, MD 21287, USA; Faculty of Medicine, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland; Landspitali University Hospital, Hringbraut, 101 Reykjavik, Iceland.
| | - Kasper D Hansen
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD 21205, USA.
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21
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Cai XJ, Wang Z, Xu YY, Yang GY, Zhang RY, Wang Y. Candesartan treatment enhances liposome penetration and anti-tumor effect via depletion of tumor stroma and normalization of tumor vessel. Drug Deliv Transl Res 2020; 11:1186-1197. [PMID: 32822012 DOI: 10.1007/s13346-020-00842-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The poor penetration of nanoparticles in solid tumors has been a critical factor limiting the clinical benefits of nanomedicine. Therefore, we depleted the dense extracellular matrix (ECM) and normalized tumor vessels to enhance drug delivery and therapeutic efficacy. We used candesartan as an angiotensin system inhibitor, which reduced ECM content and facilitated "vascular normalization" by targeting the angiotensin-signaling axis, resulting in improved anti-cancer therapeutic effects. We also combined candesartan with PEGylated liposome-encapsulated zoledronic acid (ZOL) (PEG-ZOL-LPs) to assess how this affected anti-tumor therapy. Our findings indicated that the migration of 4T1 mouse breast cancer cells was inhibited by candesartan. Moreover, the ECM depletion (including collagen I and hyaluronan) by candesartan was achieved through the downregulation of TGF-β1 in vitro, consistent with in vivo results. Furthermore, treatment groups that received candesartan also had significantly decreased tumor vessel permeability and proportions of circulating endothelial progenitor cells (CEPCs) in the serum, which resulted in normalization of tumor vasculature and improved delivery of PEG-ZOL-LPs. Finally, the positive effect candesartan in terms of tumor growth was found not to have an impact of the efficacy of the PEG-ZOL-LPs treatment. This unexpected lack of effect of candesartan on the performance of PEG-ZOL-LPs would be due to dynamics of the effect of both treatments. It might be possible that a different protocol of administration could lead to a synergistic effect. Graphical abstract The schematic illustration showed that candesartan favored depletion of tumor stroma and tumor vascular normalization to improve the anti-cancer efficacy of PEG-ZOL-LPs.
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Affiliation(s)
- Xin-Jun Cai
- Department of Pharmacy, Zhejiang Hospital of Integrated Traditional Chinese and Western Medicine, Hangzhou Red Cross Hospital, Hangzhou, 310003, Zhejiang, People's Republic of China.
| | - Zeng Wang
- Department of Pharmacy, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Ying-Ying Xu
- Department of Pharmacy, Zhejiang Hospital of Integrated Traditional Chinese and Western Medicine, Hangzhou Red Cross Hospital, Hangzhou, 310003, Zhejiang, People's Republic of China
| | - Gao-Yi Yang
- Department of Ultrasoud, Zhejiang Hospital of Integrated Traditional Chinese and Western Medicine, Hangzhou Red Cross Hospital, Hangzhou, 310003, Zhejiang, People's Republic of China
| | - Ruo-Ying Zhang
- Department of Pharmacy, Zhejiang Hospital of Integrated Traditional Chinese and Western Medicine, Hangzhou Red Cross Hospital, Hangzhou, 310003, Zhejiang, People's Republic of China
| | - Yu Wang
- Department of Pharmacy, Zhejiang Hospital of Integrated Traditional Chinese and Western Medicine, Hangzhou Red Cross Hospital, Hangzhou, 310003, Zhejiang, People's Republic of China
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22
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Zhao G, Li K, Li B, Wang Z, Fang Z, Wang X, Zhang Y, Luo T, Zhou Q, Wang L, Xie Y, Wang Y, Chen Q, Xia L, Tang Y, Tang B, Xia K, Li J. Gene4Denovo: an integrated database and analytic platform for de novo mutations in humans. Nucleic Acids Res 2020; 48:D913-D926. [PMID: 31642496 PMCID: PMC7145562 DOI: 10.1093/nar/gkz923] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/19/2019] [Accepted: 10/08/2019] [Indexed: 12/14/2022] Open
Abstract
De novo mutations (DNMs) significantly contribute to sporadic diseases, particularly in neuropsychiatric disorders. Whole-exome sequencing (WES) and whole-genome sequencing (WGS) provide effective methods for detecting DNMs and prioritizing candidate genes. However, it remains a challenge for scientists, clinicians, and biologists to conveniently access and analyse data regarding DNMs and candidate genes from scattered publications. To fill the unmet need, we integrated 580 799 DNMs, including 30 060 coding DNMs detected by WES/WGS from 23 951 individuals across 24 phenotypes and prioritized a list of candidate genes with different degrees of statistical evidence, including 346 genes with false discovery rates <0.05. We then developed a database called Gene4Denovo (http://www.genemed.tech/gene4denovo/), which allowed these genetic data to be conveniently catalogued, searched, browsed, and analysed. In addition, Gene4Denovo integrated data from >60 genomic sources to provide comprehensive variant-level and gene-level annotation and information regarding the DNMs and candidate genes. Furthermore, Gene4Denovo provides end-users with limited bioinformatics skills to analyse their own genetic data, perform comprehensive annotation, and prioritize candidate genes using custom parameters. In conclusion, Gene4Denovo conveniently allows for the accelerated interpretation of DNM pathogenicity and the clinical implication of DNMs in humans.
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Affiliation(s)
- Guihu Zhao
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Kuokuo Li
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Bin Li
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zheng Wang
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhenghuan Fang
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Xiaomeng Wang
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yi Zhang
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Tengfei Luo
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qiao Zhou
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lin Wang
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yali Xie
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yijing Wang
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qian Chen
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lu Xia
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yu Tang
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Beisha Tang
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Kun Xia
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jinchen Li
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
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23
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Hsieh A, Morton SU, Willcox JAL, Gorham JM, Tai AC, Qi H, DePalma S, McKean D, Griffin E, Manheimer KB, Bernstein D, Kim RW, Newburger JW, Porter GA, Srivastava D, Tristani-Firouzi M, Brueckner M, Lifton RP, Goldmuntz E, Gelb BD, Chung WK, Seidman CE, Seidman JG, Shen Y. EM-mosaic detects mosaic point mutations that contribute to congenital heart disease. Genome Med 2020; 12:42. [PMID: 32349777 PMCID: PMC7189690 DOI: 10.1186/s13073-020-00738-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 04/09/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The contribution of somatic mosaicism, or genetic mutations arising after oocyte fertilization, to congenital heart disease (CHD) is not well understood. Further, the relationship between mosaicism in blood and cardiovascular tissue has not been determined. METHODS We developed a new computational method, EM-mosaic (Expectation-Maximization-based detection of mosaicism), to analyze mosaicism in exome sequences derived primarily from blood DNA of 2530 CHD proband-parent trios. To optimize this method, we measured mosaic detection power as a function of sequencing depth. In parallel, we analyzed our cohort using MosaicHunter, a Bayesian genotyping algorithm-based mosaic detection tool, and compared the two methods. The accuracy of these mosaic variant detection algorithms was assessed using an independent resequencing method. We then applied both methods to detect mosaicism in cardiac tissue-derived exome sequences of 66 participants for which matched blood and heart tissue was available. RESULTS EM-mosaic detected 326 mosaic mutations in blood and/or cardiac tissue DNA. Of the 309 detected in blood DNA, 85/97 (88%) tested were independently confirmed, while 7/17 (41%) candidates of 17 detected in cardiac tissue were confirmed. MosaicHunter detected an additional 64 mosaics, of which 23/46 (50%) among 58 candidates from blood and 4/6 (67%) of 6 candidates from cardiac tissue confirmed. Twenty-five mosaic variants altered CHD-risk genes, affecting 1% of our cohort. Of these 25, 22/22 candidates tested were confirmed. Variants predicted as damaging had higher variant allele fraction than benign variants, suggesting a role in CHD. The estimated true frequency of mosaic variants above 10% mosaicism was 0.14/person in blood and 0.21/person in cardiac tissue. Analysis of 66 individuals with matched cardiac tissue available revealed both tissue-specific and shared mosaicism, with shared mosaics generally having higher allele fraction. CONCLUSIONS We estimate that ~ 1% of CHD probands have a mosaic variant detectable in blood that could contribute to cardiac malformations, particularly those damaging variants with relatively higher allele fraction. Although blood is a readily available DNA source, cardiac tissues analyzed contributed ~ 5% of somatic mosaic variants identified, indicating the value of tissue mosaicism analyses.
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Affiliation(s)
- Alexander Hsieh
- Columbia University Medical Center, 1130 St Nicholas Ave, New York, NY, 10032, USA
| | - Sarah U Morton
- Boston Children's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | | | | | | | - Hongjian Qi
- Columbia University Medical Center, 1130 St Nicholas Ave, New York, NY, 10032, USA
| | | | | | - Emily Griffin
- Columbia University Medical Center, 1130 St Nicholas Ave, New York, NY, 10032, USA
| | | | | | - Richard W Kim
- Children's Hospital Los Angeles, Los Angeles, CA, USA
| | | | | | - Deepak Srivastava
- Gladstone Institutes and University of California San Francisco, San Francisco, CA, USA
| | | | | | | | | | - Bruce D Gelb
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wendy K Chung
- Columbia University Medical Center, 1130 St Nicholas Ave, New York, NY, 10032, USA
| | - Christine E Seidman
- Harvard Medical School, Boston, MA, USA.,Brigham and Women's Hospital, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard University, Boston, MA, USA
| | | | - Yufeng Shen
- Columbia University Medical Center, 1130 St Nicholas Ave, New York, NY, 10032, USA.
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24
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Wang X, Goldstein DB. Enhancer Domains Predict Gene Pathogenicity and Inform Gene Discovery in Complex Disease. Am J Hum Genet 2020; 106:215-233. [PMID: 32032514 PMCID: PMC7010980 DOI: 10.1016/j.ajhg.2020.01.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 01/13/2020] [Indexed: 02/07/2023] Open
Abstract
Non-coding transcriptional regulatory elements are critical for controlling the spatiotemporal expression of genes. Here, we demonstrate that the sizes and number of enhancers linked to a gene reflect its disease pathogenicity. Moreover, genes with redundant enhancer domains are depleted of cis-acting genetic variants that disrupt gene expression, and they are buffered against the effects of disruptive non-coding mutations. Our results demonstrate that dosage-sensitive genes have evolved a robustness to the disruptive effects of genetic variation by expanding their regulatory domains. This solves a puzzle about why genes associated with human disease are depleted of cis-eQTLs (cis-expression quantitative trait loci), suggesting that this relationship might complicate gene identification in causal genome-wide association studies (GWASs) using eQTL information, and establishes a framework for identifying non-coding regulatory variation with phenotypic consequences.
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Affiliation(s)
- Xinchen Wang
- Institute for Genomic Medicine, Columbia University Medical Center, Hammer Health Sciences, 701 West 168th Street, New York, New York 10032, USA.
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, Hammer Health Sciences, 701 West 168th Street, New York, New York 10032, USA; Department of Genetics and Development, Columbia University Medical Center, Hammer Health Sciences, 701 West 168th Street, New York, New York 10032, USA.
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25
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Casanova EL, Switala AE, Dandamudi S, Hickman AR, Vandenbrink J, Sharp JL, Feltus FA, Casanova MF. Autism risk genes are evolutionarily ancient and maintain a unique feature landscape that echoes their function. Autism Res 2019; 12:860-869. [PMID: 31025836 PMCID: PMC6613973 DOI: 10.1002/aur.2112] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 03/22/2019] [Accepted: 04/06/2019] [Indexed: 11/09/2022]
Abstract
Previous research on autism risk (ASD), developmental regulatory (DevReg), and central nervous system (CNS) genes suggests they tend to be large in size, enriched in nested repeats, and mutation intolerant. The relevance of these genomic features is intriguing yet poorly understood. In this study, we investigated the feature landscape of these gene groups to discover structural themes useful in interpreting their function, developmental patterns, and evolutionary history. ASD, DevReg, CNS, housekeeping, and whole genome control (WGC) groups were compiled using various resources. Multiple gene features of interest were extracted from NCBI/UCSC Bioinformatics. Residual variation intolerance scores, Exome Aggregation Consortium pLI scores, and copy number variation data from Decipher were used to estimate variation intolerance. Gene age and protein-protein interactions (PPI) were estimated using Ensembl and EBI Intact databases, respectively. Compared to WGC: ASD, DevReg, and CNS genes are longer, produce larger proteins, maintain greater numbers/density of conserved noncoding elements and transposable elements, produce more transcript variants, and are comparatively variation intolerant. After controlling for gene size, mutation tolerance, and clinical association, ASD genes still retain many of these same features. In addition, we also found that ASD genes that are extremely mutation intolerant have larger PPI networks. These data support many of the recent findings within the field of autism genetics but also expand our understanding of the evolution of these broad gene groups, their potential regulatory complexity, and the extent to which they interact with the cellular network. Autism Res 2019, 12: 860-869. © 2019 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: Autism risk genes are more ancient compared to other genes in the genome. As such, they exhibit physical features related to their age, including long gene and protein size and regulatory sequences that help to control gene expression. They share many of these same features with other genes that are expressed in the brain and/or are associated with prenatal development.
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Affiliation(s)
- Emily L. Casanova
- Department of Biomedical Sciences, University of South
Carolina, South Carolina, USA
- Department of Pediatrics, Greenville Health System,
Greenville, USA
| | - Andrew E. Switala
- Department of Bioengineering, University of Louisville,
Louisville, Kentucky, USA
| | - Srini Dandamudi
- Department of Statistics, Colorado State University, Fort
Collins, Colorado, USA
| | - Allison R. Hickman
- Department of Genetics and Biochemistry, Clemson
University, Clemson, South Carolina, USA
| | | | - Julia L. Sharp
- Department of Statistics, Colorado State University, Fort
Collins, Colorado, USA
| | - F. Alex Feltus
- Department of Genetics and Biochemistry, Clemson
University, Clemson, South Carolina, USA
| | - Manuel F. Casanova
- Department of Biomedical Sciences, University of South
Carolina, South Carolina, USA
- Department of Pediatrics, Greenville Health System,
Greenville, USA
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26
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Abstract
Variably expressive copy-number variants (CNVs) are characterized by extensive phenotypic heterogeneity of neuropsychiatric phenotypes. Approaches to identify single causative genes for these phenotypes within each CNV have not been successful. Here, we posit using multiple lines of evidence, including pathogenicity metrics, functional assays of model organisms, and gene expression data, that multiple genes within each CNV region are likely responsible for the observed phenotypes. We propose that candidate genes within each region likely interact with each other through shared pathways to modulate the individual gene phenotypes, emphasizing the genetic complexity of CNV-associated neuropsychiatric features.
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Affiliation(s)
- Matthew Jensen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Bioinformatics and Genomics Program, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Santhosh Girirajan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Bioinformatics and Genomics Program, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, United States of America
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