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Barker CIS, Groeneweg G, Maitland-van der Zee AH, Rieder MJ, Hawcutt DB, Hubbard TJ, Swen JJ, Carleton BC. Pharmacogenomic testing in paediatrics: clinical implementation strategies. Br J Clin Pharmacol 2021; 88:4297-4310. [PMID: 34907575 PMCID: PMC9544158 DOI: 10.1111/bcp.15181] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 10/22/2021] [Accepted: 11/09/2021] [Indexed: 11/27/2022] Open
Abstract
Pharmacogenomics (PGx) relates to the study of genetic factors determining variability in drug response. Implementing PGx testing in paediatric patients can enhance drug safety, helping to improve drug efficacy or reduce the risk of toxicity. Despite its clinical relevance, the implementation of PGx testing in paediatric practice to date has been variable and limited. As with most paediatric pharmacological studies, there are well‐recognised barriers to obtaining high‐quality PGx evidence, particularly when patient numbers may be small, and off‐label or unlicensed prescribing remains widespread. Furthermore, trials enrolling small numbers of children can rarely, in isolation, provide sufficient PGx evidence to change clinical practice, so extrapolation from larger PGx studies in adult patients, where scientifically sound, is essential. This review paper discusses the relevance of PGx to paediatrics and considers implementation strategies from a child health perspective. Examples are provided from Canada, the Netherlands and the UK, with consideration of the different healthcare systems and their distinct approaches to implementation, followed by future recommendations based on these cumulative experiences. Improving the evidence base demonstrating the clinical utility and cost‐effectiveness of paediatric PGx testing will be critical to drive implementation forwards. International, interdisciplinary collaborations will enhance paediatric data collation, interpretation and evidence curation, while also supporting dedicated paediatric PGx educational initiatives. PGx consortia and paediatric clinical research networks will continue to play a central role in the streamlined development of effective PGx implementation strategies to help optimise paediatric pharmacotherapy.
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Affiliation(s)
- Charlotte I S Barker
- Department of Medical & Molecular Genetics, King's College London, London, UK.,Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Gabriella Groeneweg
- Division of Translational Therapeutics, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada.,Pharmaceutical Outcomes Programme, BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Anke H Maitland-van der Zee
- Respiratory Medicine/Pediatric Respiratory Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Michael J Rieder
- Departments of Paediatrics, Physiology and Pharmacology and Medicine, Western University, London, Ontario, Canada.,Molecular Medicine Group, Robarts Research Institute, London, Ontario, Canada
| | - Daniel B Hawcutt
- Department of Women's and Children's Health, University of Liverpool, Liverpool, UK.,NIHR Clinical Research Facility, Alder Hey Children's Hospital, Liverpool, UK
| | - Tim J Hubbard
- Department of Medical & Molecular Genetics, King's College London, London, UK.,Genomics England, London, UK
| | - Jesse J Swen
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands.,Leiden Network for Personalized Therapeutics, Leiden, The Netherlands
| | - Bruce C Carleton
- Division of Translational Therapeutics, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada.,Pharmaceutical Outcomes Programme, BC Children's Hospital, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
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2
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Geihs M, Yan Y, Walter K, Huang J, Memari Y, Min JL, Mead D, Hubbard TJ, Timpson NJ, Down TA, Soranzo N. An interactive genome browser of association results from the UK10K cohorts project. Bioinformatics 2015; 31:4029-31. [PMID: 26315906 PMCID: PMC4673976 DOI: 10.1093/bioinformatics/btv491] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 08/17/2015] [Indexed: 11/12/2022] Open
Abstract
UNLABELLED High-throughput sequencing technologies survey genetic variation at genome scale and are increasingly used to study the contribution of rare and low-frequency genetic variants to human traits. As part of the Cohorts arm of the UK10K project, genetic variants called from low-read depth (average 7×) whole genome sequencing of 3621 cohort individuals were analysed for statistical associations with 64 different phenotypic traits of biomedical importance. Here, we describe a novel genome browser based on the Biodalliance platform developed to provide interactive access to the association results of the project. AVAILABILITY AND IMPLEMENTATION The browser is available at http://www.uk10k.org/dalliance.html. Source code for the Biodalliance platform is available under a BSD license from http://github.com/dasmoth/dalliance, and for the LD-display plugin and backend from http://github.com/dasmoth/ldserv.
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Affiliation(s)
- Matthias Geihs
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton CB10 1HH, UK
| | - Ying Yan
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton CB10 1HH, UK
| | - Klaudia Walter
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton CB10 1HH, UK
| | - Jie Huang
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton CB10 1HH, UK
| | - Yasin Memari
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton CB10 1HH, UK
| | - Josine L Min
- MRC Integrative Epidemiology Unit, University of Bristol, Oakfield Grove, Bristol, UK
| | - Daniel Mead
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton CB10 1HH, UK
| | | | - Tim J Hubbard
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton CB10 1HH, UK, Department of Medical and Molecular Genetics, Division of Genetics and Molecular Medicine, King's College London School of Medicine, Guy's Hospital, London SE1 9RT, UK
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Oakfield Grove, Bristol, UK
| | | | - Nicole Soranzo
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton CB10 1HH, UK, Department of Haematology, University of Cambridge, Cambridge CB2 1TN, UK
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3
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Steijger T, Abril JF, Engström PG, Kokocinski F, Hubbard TJ, Guigó R, Harrow J, Bertone P. Assessment of transcript reconstruction methods for RNA-seq. Nat Methods 2013; 10:1177-84. [PMID: 24185837 PMCID: PMC3851240 DOI: 10.1038/nmeth.2714] [Citation(s) in RCA: 447] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Accepted: 09/23/2013] [Indexed: 11/09/2022]
Abstract
We evaluated 25 protocol variants of 14 independent computational methods for exon identification, transcript reconstruction and expression-level quantification from RNA-seq data. Our results show that most algorithms are able to identify discrete transcript components with high success rates but that assembly of complete isoform structures poses a major challenge even when all constituent elements are identified. Expression-level estimates also varied widely across methods, even when based on similar transcript models. Consequently, the complexity of higher eukaryotic genomes imposes severe limitations on transcript recall and splice product discrimination that are likely to remain limiting factors for the analysis of current-generation RNA-seq data.
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Affiliation(s)
- Tamara Steijger
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Josep F Abril
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Pär G Engström
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | | | | | - Roderic Guigó
- Center for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Paul Bertone
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
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4
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Koohy H, Down TA, Hubbard TJ. Chromatin accessibility data sets show bias due to sequence specificity of the DNase I enzyme. PLoS One 2013; 8:e69853. [PMID: 23922824 PMCID: PMC3724795 DOI: 10.1371/journal.pone.0069853] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 06/12/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND DNase I is an enzyme which cuts duplex DNA at a rate that depends strongly upon its chromatin environment. In combination with high-throughput sequencing (HTS) technology, it can be used to infer genome-wide landscapes of open chromatin regions. Using this technology, systematic identification of hundreds of thousands of DNase I hypersensitive sites (DHS) per cell type has been possible, and this in turn has helped to precisely delineate genomic regulatory compartments. However, to date there has been relatively little investigation into possible biases affecting this data. RESULTS We report a significant degree of sequence preference spanning sites cut by DNase I in a number of published data sets. The two major protocols in current use each show a different pattern, but for a given protocol the pattern of sequence specificity seems to be quite consistent. The patterns are substantially different from biases seen in other types of HTS data sets, and in some cases the most constrained position lies outside the sequenced fragment, implying that this constraint must relate to the digestion process rather than events occurring during library preparation or sequencing. CONCLUSIONS DNase I is a sequence-specific enzyme, with a specificity that may depend on experimental conditions. This sequence specificity is not taken into account by existing pipelines for identifying open chromatin regions. Care must be taken when interpreting DNase I results, especially when looking at the precise locations of the reads. Future studies may be able to improve the sensitivity and precision of chromatin state measurement by compensating for sequence bias.
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Affiliation(s)
- Hashem Koohy
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.
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5
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Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, Rodriguez JM, Ezkurdia I, van Baren J, Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guigó R, Hubbard TJ. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res 2013; 22:1760-74. [PMID: 22955987 PMCID: PMC3431492 DOI: 10.1101/gr.135350.111] [Citation(s) in RCA: 3491] [Impact Index Per Article: 317.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers.
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Affiliation(s)
- Jennifer Harrow
- Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.
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6
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Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigó R. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 2013; 22:1775-89. [PMID: 22955988 PMCID: PMC3431493 DOI: 10.1101/gr.132159.111] [Citation(s) in RCA: 3740] [Impact Index Per Article: 340.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The human genome contains many thousands of long noncoding RNAs (lncRNAs). While several studies have demonstrated compelling biological and disease roles for individual examples, analytical and experimental approaches to investigate these genes have been hampered by the lack of comprehensive lncRNA annotation. Here, we present and analyze the most complete human lncRNA annotation to date, produced by the GENCODE consortium within the framework of the ENCODE project and comprising 9277 manually annotated genes producing 14,880 transcripts. Our analyses indicate that lncRNAs are generated through pathways similar to that of protein-coding genes, with similar histone-modification profiles, splicing signals, and exon/intron lengths. In contrast to protein-coding genes, however, lncRNAs display a striking bias toward two-exon transcripts, they are predominantly localized in the chromatin and nucleus, and a fraction appear to be preferentially processed into small RNAs. They are under stronger selective pressure than neutrally evolving sequences—particularly in their promoter regions, which display levels of selection comparable to protein-coding genes. Importantly, about one-third seem to have arisen within the primate lineage. Comprehensive analysis of their expression in multiple human organs and brain regions shows that lncRNAs are generally lower expressed than protein-coding genes, and display more tissue-specific expression patterns, with a large fraction of tissue-specific lncRNAs expressed in the brain. Expression correlation analysis indicates that lncRNAs show particularly striking positive correlation with the expression of antisense coding genes. This GENCODE annotation represents a valuable resource for future studies of lncRNAs.
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Affiliation(s)
- Thomas Derrien
- Bioinformatics and Genomics, Centre for Genomic Regulation and UPF, 08003 Barcelona, Catalonia, Spain
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7
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Pei B, Sisu C, Frankish A, Howald C, Habegger L, Mu XJ, Harte R, Balasubramanian S, Tanzer A, Diekhans M, Reymond A, Hubbard TJ, Harrow J, Gerstein MB. The GENCODE pseudogene resource. Genome Biol 2012; 13:R51. [PMID: 22951037 PMCID: PMC3491395 DOI: 10.1186/gb-2012-13-9-r51] [Citation(s) in RCA: 253] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 05/30/2012] [Accepted: 06/25/2012] [Indexed: 12/11/2022] Open
Abstract
Background Pseudogenes have long been considered as nonfunctional genomic sequences. However, recent evidence suggests that many of them might have some form of biological activity, and the possibility of functionality has increased interest in their accurate annotation and integration with functional genomics data. Results As part of the GENCODE annotation of the human genome, we present the first genome-wide pseudogene assignment for protein-coding genes, based on both large-scale manual annotation and in silico pipelines. A key aspect of this coupled approach is that it allows us to identify pseudogenes in an unbiased fashion as well as untangle complex events through manual evaluation. We integrate the pseudogene annotations with the extensive ENCODE functional genomics information. In particular, we determine the expression level, transcription-factor and RNA polymerase II binding, and chromatin marks associated with each pseudogene. Based on their distribution, we develop simple statistical models for each type of activity, which we validate with large-scale RT-PCR-Seq experiments. Finally, we compare our pseudogenes with conservation and variation data from primate alignments and the 1000 Genomes project, producing lists of pseudogenes potentially under selection. Conclusions At one extreme, some pseudogenes possess conventional characteristics of functionality; these may represent genes that have recently died. On the other hand, we find interesting patterns of partial activity, which may suggest that dead genes are being resurrected as functioning non-coding RNAs. The activity data of each pseudogene are stored in an associated resource, psiDR, which will be useful for the initial identification of potentially functional pseudogenes.
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Affiliation(s)
- Baikang Pei
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
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8
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Howald C, Tanzer A, Chrast J, Kokocinski F, Derrien T, Walters N, Gonzalez JM, Frankish A, Aken BL, Hourlier T, Vogel JH, White S, Searle S, Harrow J, Hubbard TJ, Guigó R, Reymond A. Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome. Genome Res 2012; 22:1698-710. [PMID: 22955982 PMCID: PMC3431487 DOI: 10.1101/gr.134478.111] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 05/01/2012] [Indexed: 12/21/2022]
Abstract
Within the ENCODE Consortium, GENCODE aimed to accurately annotate all protein-coding genes, pseudogenes, and noncoding transcribed loci in the human genome through manual curation and computational methods. Annotated transcript structures were assessed, and less well-supported loci were systematically, experimentally validated. Predicted exon-exon junctions were evaluated by RT-PCR amplification followed by highly multiplexed sequencing readout, a method we called RT-PCR-seq. Seventy-nine percent of all assessed junctions are confirmed by this evaluation procedure, demonstrating the high quality of the GENCODE gene set. RT-PCR-seq was also efficient to screen gene models predicted using the Human Body Map (HBM) RNA-seq data. We validated 73% of these predictions, thus confirming 1168 novel genes, mostly noncoding, which will further complement the GENCODE annotation. Our novel experimental validation pipeline is extremely sensitive, far more than unbiased transcriptome profiling through RNA sequencing, which is becoming the norm. For example, exon-exon junctions unique to GENCODE annotated transcripts are five times more likely to be corroborated with our targeted approach than with extensive large human transcriptome profiling. Data sets such as the HBM and ENCODE RNA-seq data fail sampling of low-expressed transcripts. Our RT-PCR-seq targeted approach also has the advantage of identifying novel exons of known genes, as we discovered unannotated exons in ~11% of assessed introns. We thus estimate that at least 18% of known loci have yet-unannotated exons. Our work demonstrates that the cataloging of all of the genic elements encoded in the human genome will necessitate a coordinated effort between unbiased and targeted approaches, like RNA-seq and RT-PCR-seq.
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Affiliation(s)
- Cédric Howald
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Andrea Tanzer
- Centre de Regulacio Genomica, Grup de Recerca en Informatica Biomedica, E-08003 Barcelona, Spain
| | - Jacqueline Chrast
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Felix Kokocinski
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Thomas Derrien
- Centre de Regulacio Genomica, Grup de Recerca en Informatica Biomedica, E-08003 Barcelona, Spain
| | - Nathalie Walters
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Jose M. Gonzalez
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Adam Frankish
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Bronwen L. Aken
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Thibaut Hourlier
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Jan-Hinnerk Vogel
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Simon White
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Stephen Searle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Jennifer Harrow
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Tim J. Hubbard
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Roderic Guigó
- Centre de Regulacio Genomica, Grup de Recerca en Informatica Biomedica, E-08003 Barcelona, Spain
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
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Coffey AJ, Kokocinski F, Calafato MS, Scott CE, Palta P, Drury E, Joyce CJ, Leproust EM, Harrow J, Hunt S, Lehesjoki AE, Turner DJ, Hubbard TJ, Palotie A. The GENCODE exome: sequencing the complete human exome. Eur J Hum Genet 2011; 19:827-31. [PMID: 21364695 PMCID: PMC3137498 DOI: 10.1038/ejhg.2011.28] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Sequencing the coding regions, the exome, of the human genome is one of the major current strategies to identify low frequency and rare variants associated with human disease traits. So far, the most widely used commercial exome capture reagents have mainly targeted the consensus coding sequence (CCDS) database. We report the design of an extended set of targets for capturing the complete human exome, based on annotation from the GENCODE consortium. The extended set covers an additional 5594 genes and 10.3 Mb compared with the current CCDS-based sets. The additional regions include potential disease genes previously inaccessible to exome resequencing studies, such as 43 genes linked to ion channel activity and 70 genes linked to protein kinase activity. In total, the new GENCODE exome set developed here covers 47.9 Mb and performed well in sequence capture experiments. In the sample set used in this study, we identified over 5000 SNP variants more in the GENCODE exome target (24%) than in the CCDS-based exome sequencing.
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Affiliation(s)
- Alison J Coffey
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
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10
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Boles MK, Wilkinson BM, Wilming LG, Liu B, Probst FJ, Harrow J, Grafham D, Hentges KE, Woodward LP, Maxwell A, Mitchell K, Risley MD, Johnson R, Hirschi K, Lupski JR, Funato Y, Miki H, Marin-Garcia P, Matthews L, Coffey AJ, Parker A, Hubbard TJ, Rogers J, Bradley A, Adams DJ, Justice MJ. Discovery of candidate disease genes in ENU-induced mouse mutants by large-scale sequencing, including a splice-site mutation in nucleoredoxin. PLoS Genet 2009; 5:e1000759. [PMID: 20011118 PMCID: PMC2782131 DOI: 10.1371/journal.pgen.1000759] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Accepted: 11/09/2009] [Indexed: 12/13/2022] Open
Abstract
An accurate and precisely annotated genome assembly is a fundamental requirement for functional genomic analysis. Here, the complete DNA sequence and gene annotation of mouse Chromosome 11 was used to test the efficacy of large-scale sequencing for mutation identification. We re-sequenced the 14,000 annotated exons and boundaries from over 900 genes in 41 recessive mutant mouse lines that were isolated in an N-ethyl-N-nitrosourea (ENU) mutation screen targeted to mouse Chromosome 11. Fifty-nine sequence variants were identified in 55 genes from 31 mutant lines. 39% of the lesions lie in coding sequences and create primarily missense mutations. The other 61% lie in noncoding regions, many of them in highly conserved sequences. A lesion in the perinatal lethal line l11Jus13 alters a consensus splice site of nucleoredoxin (Nxn), inserting 10 amino acids into the resulting protein. We conclude that point mutations can be accurately and sensitively recovered by large-scale sequencing, and that conserved noncoding regions should be included for disease mutation identification. Only seven of the candidate genes we report have been previously targeted by mutation in mice or rats, showing that despite ongoing efforts to functionally annotate genes in the mammalian genome, an enormous gap remains between phenotype and function. Our data show that the classical positional mapping approach of disease mutation identification can be extended to large target regions using high-throughput sequencing.
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Affiliation(s)
- Melissa K. Boles
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Bonney M. Wilkinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Laurens G. Wilming
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Bin Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Frank J. Probst
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jennifer Harrow
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Darren Grafham
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Kathryn E. Hentges
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Lanette P. Woodward
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Andrea Maxwell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Karen Mitchell
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Michael D. Risley
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Randy Johnson
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Karen Hirschi
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children's Hospital, Houston, Texas, United States of America
| | - Yosuke Funato
- Laboratory of Intracellular Signaling, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Hiroaki Miki
- Laboratory of Intracellular Signaling, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Pablo Marin-Garcia
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Lucy Matthews
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Alison J. Coffey
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Anne Parker
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Tim J. Hubbard
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Jane Rogers
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Allan Bradley
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - David J. Adams
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
- * E-mail: (MJJ); (DJA)
| | - Monica J. Justice
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail: (MJJ); (DJA)
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11
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Uren AG, Kool J, Matentzoglu K, de Ridder J, Mattison J, van Uitert M, Lagcher W, Sie D, Tanger E, Cox T, Reinders M, Hubbard TJ, Rogers J, Jonkers J, Wessels L, Adams DJ, van Lohuizen M, Berns A. Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks. Cell 2008; 133:727-41. [PMID: 18485879 PMCID: PMC2405818 DOI: 10.1016/j.cell.2008.03.021] [Citation(s) in RCA: 158] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Revised: 01/21/2008] [Accepted: 03/10/2008] [Indexed: 01/25/2023]
Abstract
p53 and p19(ARF) are tumor suppressors frequently mutated in human tumors. In a high-throughput screen in mice for mutations collaborating with either p53 or p19(ARF) deficiency, we identified 10,806 retroviral insertion sites, implicating over 300 loci in tumorigenesis. This dataset reveals 20 genes that are specifically mutated in either p19(ARF)-deficient, p53-deficient or wild-type mice (including Flt3, mmu-mir-106a-363, Smg6, and Ccnd3), as well as networks of significant collaborative and mutually exclusive interactions between cancer genes. Furthermore, we found candidate tumor suppressor genes, as well as distinct clusters of insertions within genes like Flt3 and Notch1 that induce mutants with different spectra of genetic interactions. Cross species comparative analysis with aCGH data of human cancer cell lines revealed known and candidate oncogenes (Mmp13, Slamf6, and Rreb1) and tumor suppressors (Wwox and Arfrp2). This dataset should prove to be a rich resource for the study of genetic interactions that underlie tumorigenesis.
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Affiliation(s)
- Anthony G Uren
- Division of Molecular Genetics and Cancer Genomics Centre, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
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12
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Kaminski TW, Buckley BD, Powers ME, Hubbard TJ, Ortiz C. Effect of strength and proprioception training on eversion to inversion strength ratios in subjects with unilateral functional ankle instability. Br J Sports Med 2004; 37:410-5; discussion 415. [PMID: 14514531 PMCID: PMC1751367 DOI: 10.1136/bjsm.37.5.410] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
OBJECTIVES To examine the effect of six weeks of strength and proprioception training on eversion to inversion isokinetic strength ratios (E/I ratios) in subjects with unilateral functional ankle instability. METHODS Thirty eight subjects were randomly assigned to one of four treatment groups: strength training (S); proprioception training (P); strength + proprioception training (B); control (C). Isokinetic strength was tested before and after training using a Kin Com 125 automatic positioning isokinetic dynamometer. Subtalar joint eversion and inversion motions were tested both concentrically and eccentrically through a range of motion involving 40 degrees. All peak torque and average torque values were normalised for body mass. E/I ratios were calculated from average torque and peak torque measures by taking the concentric eversion value and combining it with the eccentric inversion value. Data were analysed using a mixed model analysis of variance with repeated measures on the test factor. Average torque and peak torque E/I ratios at 30 and 120 degrees/s were analysed separately. RESULTS There were no significant differences in average torque and peak torque E/I ratios of the functionally unstable ankle for any of the groups after training compared with before. CONCLUSIONS Six weeks of strength and proprioception training (either alone or combined) had no effect on isokinetic measures of strength in subjects with self reported unilateral functional instability. Further studies examining this agonist (concentric) to antagonist (eccentric) muscle group strength ratio are needed.
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Affiliation(s)
- T W Kaminski
- Sports Medicine and Athletic Training Department, Southwest Missouri State University, Springfield, Missouri, USA.
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13
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Affiliation(s)
- A Murzin
- Centre for Protein Engineering, MRC Centre, Cambridge, UK
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14
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Lesk AM, Lo Conte L, Hubbard TJ. Assessment of novel fold targets in CASP4: predictions of three-dimensional structures, secondary structures, and interresidue contacts. Proteins 2002; Suppl 5:98-118. [PMID: 11835487 DOI: 10.1002/prot.10056] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In the Novel Fold category, three types of predictions were assessed: three-dimensional structures, secondary structures, and residue-residue contacts. For predictions of three-dimensional models, CASP4 targets included 5 domains or structures with novel folds, and 13 on the borderline between Novel Fold and Fold Recognition categories. These elicited 1863 predictions of these and other targets by methods more general than comparative modeling or fold recognition techniques. The group of Bonneau, Tsai, Ruczinski, and Baker stood out as performing well with the greatest consistency. In many cases, several groups were able to predict fragments of the target correctly-often at a level somewhat larger than standard supersecondary structures-but were not able to assemble fragments into a correct global topology. The methods of Bonneau, Tsai, Ruczinski, and Baker have been successful in addressing the fragment assembly problem for many but not all the target structures.
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Affiliation(s)
- A M Lesk
- Department of Haematology, University of Cambridge Clinical School, Cambridge Institute for Medical Research, Cambridge, United Kingdom.
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15
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Hubbard TJ. Positioning of the nasal tip. Plast Reconstr Surg 2001; 108:587. [PMID: 11496226 DOI: 10.1097/00006534-200108000-00072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Hubbard TJ. Asymmetric breast implant levels. Plast Reconstr Surg 2001; 107:1918. [PMID: 11396496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
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17
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Abstract
Now that the draft human genome sequence is available, everyone wants to be able to use it. However, we have perhaps become complacent about our ability to turn new genomes into lists of genes. The higher volume of data associated with a larger genome is accompanied by a much greater increase in complexity. We need to appreciate both the scale of the challenge of vertebrate genome analysis and the limitations of current gene prediction methods and understanding.
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Affiliation(s)
- E Birney
- The European Bioinformatics Institute, Hinxton, Cambridge, UK.
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18
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Abstract
SUMMARY We have written a fully extensible Java application for visually browsing expression data, and clusters of genes or experimental conditions calculated from that data. The application requires a run-time environment for Java2. AVAILABILITY http://www. sanger.ac.uk/Users/mrp/java/ExpressionBrowser
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Affiliation(s)
- M R Pocock
- The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
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19
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Abstract
Manipulating tip projection and rotation is among the greater challenges in aesthetic surgery. Among common current techniques such as columellar struts and projecting tip grafts, all have considerable failure rates and/or complications. Powerful static and dynamic forces act on the tip, and unfortunately their magnitude and direction vary greatly from the time of surgery when decisions are made to the postoperative period. Traditional techniques have not taken sufficient advantage of the one neighboring stable structure--the septum. Through direct straddling, the medial crura on the septum or the more commonly applicable septal extension graft, tip placement at the end of surgery will vary minimally postoperatively.
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20
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Abstract
The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of known protein structures. The classification is on hierarchical levels: the first two levels, family and superfamily, describe near and distant evolutionary relationships; the third, fold, describes geometrical relationships. The distinction between evolutionary relationships and those that arise from the physics and chemistry of proteins is a feature that is unique to this database so far. The sequences of proteins in SCOP provide the basis of the ASTRAL sequence libraries that can be used as a source of data to calibrate sequence search algorithms and for the generation of statistics on, or selections of, protein structures. Links can be made from SCOP to PDB-ISL: a library containing sequences homologous to proteins of known structure. Sequences of proteins of unknown structure can be matched to distantly related proteins of known structure by using pairwise sequence comparison methods to find homologues in PDB-ISL. The database and its associated files are freely accessible from a number of WWW sites mirrored from URL http://scop.mrc-lmb.cam.ac.uk/scop/
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Affiliation(s)
- L Lo Conte
- MRC Laboratory of Molecular Biology, Centre for Protein Engineering, Hills Road, Cambridge CB2 2QH, UK.
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21
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Abstract
Evaluating a set of protein structure predictions is difficult as each prediction may omit different residues and different parts of the structure may have different accuracies. A method is described that captures the best results from a large number of alternative sequence-dependent structural superpositions between a prediction and the experimental structure and represents them as a single line on a graph. Applied to CASP2 and CASP3 data the best predictions stand out visually in most cases, as judged by manual inspection. The results from this method applied to CASP data are available from the URLs http:/(/)PredictionCenter. llnl.gov/casp3/results/th/ and http:/(/)www.sanger.ac.uk/ approximately th/casp/.
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Affiliation(s)
- T J Hubbard
- Sanger Centre, Hinxton, Cambridgeshire, United Kingdom.
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22
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Abstract
The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of all known proteins structures. The classification is on hierarchical levels: the first two levels, family and superfamily, describe near and far evolutionary relationships; the third, fold, describes geometrical relationships. The distinction between evolutionary relationships and those that arise from the physics and chemistry of proteins is a feature that is unique to this database, so far. The database can be used as a source of data to calibrate sequence search algorithms and for the generation of population statistics on protein structures. The database and its associated files are freely accessible from a number of WWW sites mirrored from URL http://scop. mrc-lmb.cam.ac.uk/scop/
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Affiliation(s)
- T J Hubbard
- Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
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23
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Hubbard TJ, Ailey B, Brenner SE, Murzin AG, Chothia C. SCOP, Structural Classification of Proteins database: applications to evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data. Acta Crystallogr D Biol Crystallogr 1998; 54:1147-54. [PMID: 10089491 DOI: 10.1107/s0907444998009172] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of all known protein structures. The classification is on hierarchical levels: the first two levels, family and superfamily, describe near and far evolutionary relationships; the third, fold, describes geometrical relationships. The distinction between evolutionary relationships and those that arise from the physics and chemistry of proteins is a feature that is unique to this database, so far. The database can be used as a source of data to calibrate sequence search algorithms and for the generation of population statistics on protein structures. The database and its associated files are freely accessible from a number of WWW sites mirrored from URL http://scop. mrc-lmb.cam.ac.uk/scop/.
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Affiliation(s)
- T J Hubbard
- Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, England.
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24
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Hubbard TJ. Closed correction of convexity of the lateral crura. Plast Reconstr Surg 1998; 102:919-20. [PMID: 9727470 DOI: 10.1097/00006534-199809030-00057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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25
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Brenner SE, Chothia C, Hubbard TJ. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc Natl Acad Sci U S A 1998; 95:6073-8. [PMID: 9600919 PMCID: PMC27587 DOI: 10.1073/pnas.95.11.6073] [Citation(s) in RCA: 360] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Pairwise sequence comparison methods have been assessed using proteins whose relationships are known reliably from their structures and functions, as described in the SCOP database [Murzin, A. G., Brenner, S. E., Hubbard, T. & Chothia C. (1995) J. Mol. Biol. 247, 536-540]. The evaluation tested the programs BLAST [Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990). J. Mol. Biol. 215, 403-410], WU-BLAST2 [Altschul, S. F. & Gish, W. (1996) Methods Enzymol. 266, 460-480], FASTA [Pearson, W. R. & Lipman, D. J. (1988) Proc. Natl. Acad. Sci. USA 85, 2444-2448], and SSEARCH [Smith, T. F. & Waterman, M. S. (1981) J. Mol. Biol. 147, 195-197] and their scoring schemes. The error rate of all algorithms is greatly reduced by using statistical scores to evaluate matches rather than percentage identity or raw scores. The E-value statistical scores of SSEARCH and FASTA are reliable: the number of false positives found in our tests agrees well with the scores reported. However, the P-values reported by BLAST and WU-BLAST2 exaggerate significance by orders of magnitude. SSEARCH, FASTA ktup = 1, and WU-BLAST2 perform best, and they are capable of detecting almost all relationships between proteins whose sequence identities are >30%. For more distantly related proteins, they do much less well; only one-half of the relationships between proteins with 20-30% identity are found. Because many homologs have low sequence similarity, most distant relationships cannot be detected by any pairwise comparison method; however, those which are identified may be used with confidence.
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Affiliation(s)
- S E Brenner
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom.
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26
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Abstract
As part of the CASP2 protein structure prediction experiment, a set of numerical criteria were defined for the evaluation of "ab initio" predictions. The evaluation package comprises a series of electronic submission formats, a submission validator, evaluation software, and a series of scripts to summarize the results for the CASP2 meeting and for presentation via the World Wide Web (WWW). The evaluation package is accessible for use on new predictions via WWW so that results can be compared to those submitted to CASP2. With further input from the community, the evaluation criteria are expected to evolve into a comprehensive set of measures capturing the overall quality of a prediction as well as critical detail essential for further development of prediction methods. We discuss present measures, limitations of the current criteria, and possible improvements.
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Affiliation(s)
- A Zemla
- Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
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27
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Abstract
In certain ethnic noses with a relative lack of dorsal projection, patients often request a narrowed appearance on frontal view. There is little debate about the benefits of dorsal augmentation, but considerable disagreement about concomitant osteotomies. In a series of six African-American and Asian rhinoplasties, the author has addressed the wide-bridge appearance with dorsal augmentation alone, without osteotomies. Gore-Tex or cartilage was used for the augmentation. All patients were satisfied with the apparent bridge narrowing on frontal view.
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Affiliation(s)
- T J Hubbard
- The Mladick Center for Plastic Surgery, Virginia Beach, VA 23454, USA
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28
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Abstract
Structural classifications aid the interpretation of proteins by describing degrees of structural and evolutionary relatedness. They have also recently revealed strikingly skewed distributions at all levels; for example, a small number of folds are far more common than others, and just a few superfamilies are known to have diverged widely. The classifications also provide an indication of the total number of superfamilies in nature.
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Affiliation(s)
- S E Brenner
- Structural Biology Centre, National Institute for Bioscience and Human-Technology, Ibaraki, Japan.
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29
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Abstract
An ever increasing number of protein sequences are being compared, partly because of the availability of full sets of protein sequences from several completed genome-sequencing projects. The resulting problem of scale has shifted the emphasis of sequence analysis method development from sensitivity and flexibility, which relies on manual intervention and interpretation, to the automatic generation of results of known reliability.
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Affiliation(s)
- T J Hubbard
- Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
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30
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Abstract
The S1 domain, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the E. coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site. The structure of the S1 domain is very similar to that of cold shock protein, suggesting that they are both derived from an ancient nucleic acid-binding protein. Enhanced sequence searches reveal hitherto unidentified S1 domains in RNase E, RNase II, NusA, EMB-5, and other proteins.
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Affiliation(s)
- M Bycroft
- Department of Chemistry, University of Cambridge, United Kingdom
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31
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32
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Abstract
The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of all known proteins structures. The classification is on hierarchical levels: the first two levels, family and superfamily, describe near and far evolutionary relationships; the third, fold, describes geometrical relationships. The distinction between evolutionary relationships and those that arise from the physics and chemistry of proteins is a feature that is unique to this database, so far. SCOP also provides for each structure links to atomic co-ordinates, images of the structures, interactive viewers, sequence data, data on any conformational changes related to function and literature references. The database is freely accessible on the World Wide Web (WWW) with an entry point at URL http://scop.mrc-lmb.cam.ac.uk/scop/
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Affiliation(s)
- T J Hubbard
- MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, UK
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33
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34
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Affiliation(s)
- S E Brenner
- Medical Research Council Centre Laboratories of Molecular Biology, Cambridge United Kingdom
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35
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Abstract
Protein structure predictions were submitted for 9 of the target sequences in the competition that ran during 1994. Targets sequences were selected that had no known homology with any sequence of known structure and were members of a reasonably sized family of related but divergent sequences. The objective was either to recognize a compatible fold for the target sequence in the database of known structures or to predict ab initio its rough 3D topology. The main tools used were Hidden Markov models (HMM) for fold recognition, a beta-strand pair potential to predict beta-sheet topology, and the PHD server for secondary structure prediction. Compatible folds were correctly identified in a number of cases and the beta-strand pair potential was shown to be a useful tool for ab initio topology prediction.
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Affiliation(s)
- T J Hubbard
- Centre for Protein Engineering (CPE), MRC Centre, Cambridge, UK
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36
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Hubbard TJ. Re: Minimal expansion for correction of male pattern baldness. Ann Plast Surg 1995; 35:441. [PMID: 8585691 DOI: 10.1097/00000637-199510000-00021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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37
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Valencia A, Hubbard TJ, Muga A, Bañuelos S, Llorca O, Carrascosa JL, Valpuesta JM. Prediction of the structure of GroES and its interaction with GroEL. Proteins 1995; 22:199-209. [PMID: 7479694 DOI: 10.1002/prot.340220302] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The three-dimensional structure of the GroES monomer and its interaction with GroEL has been predicted using a combination of prediction tools and experimental data obtained by biophysical [electron microscope (EM), Fourier transform infrared (FTIR), and nuclear magnetic resonance (NMR)] and biochemical techniques. The GroES monomer, according to the prediction, is composed of eight beta-strands forming a beta-barrel with loose ends. In the model, beta-strands 5-8 run along the outer surface of GroES, forming an antiparallel beta-sheet with beta 4 loosely bound to one of the edges. beta-strands 1-3 would then be parallel and placed in the interior of the molecule. Loops 1-3 would face the internal cavity of the GroEL-GroES complex, and together with conserved residues in loops 5 and 7, would form the active surface interacting with GroEL.
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Affiliation(s)
- A Valencia
- Centro Nacional de Biotecnología, C.S.I.C. Universidad Autónoma de Madrid, Spain
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38
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Abstract
Recreational rocket injuries can result in massive destruction of facial soft tissues and bone and can produce long-term sequelae. This study reviews the cases of three patients who arrived at our medical center within a 3-week period in July 1990 who sustained severe craniofacial injuries from fireworks. A timely multidisciplinary approach is important in the care of these injuries, since there are usually associated serious ophthalmologic and cranial injuries that require immediate attention. We present the management dilemmas confronting the personnel who treat such injuries as well as tips on avoiding long-term complications.
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Affiliation(s)
- T J Hubbard
- Division of Plastic and Reconstructive Surgery, Loyola University Medical Center, Maywood, Illinois 60153
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39
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Abstract
Recently some heat-shock proteins have been linked to functions of 'chaperoning' protein folding in vivo. Here current experimental evidence is reviewed and possible requirements for such an activity are discussed. It is proposed that one mode of chaperone action is to actively unfold misfolded or badly aggregated proteins to a conformation from which they could refold spontaneously; that improperly folded proteins are recognized by excessive stretches of solvent-exposed backbone, rather than by exposed hydrophobic patches; and that the molecular mechanism for unfolding is either repeated binding and dissociation ('plucking') or translocation of the protein backbone through a binding cleft ('threading'), allowing the threaded chain to refold spontaneously. The observed hydrolysis of ATP would provide the energy for active unfolding. These hypotheses can be applied to both monomeric folding and oligomeric assembly and are sufficiently detailed to be open to directed experimental verification.
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Affiliation(s)
- T J Hubbard
- Protein Engineering Research Institute, Osaka, Japan
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40
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Abstract
The three-dimensional structures of 41 homologous proteins (belonging to eight families) were compared by pairwise superposition. A subset of 'core' residues was defined as those whose side chains have less than 7% of their surface exposed to solvent. This subset has significantly higher sequence identity and lower root mean square (RMS) alpha carbon separation than for all topologically equivalent residues in the structure, when members of a protein family are superposed. For such superpositions the relationship between RMS distance and percentage sequence identity of this subset of residues is similar to that for all equivalent residues, although some variation is observed between families of proteins which are predominantly beta sheet and those which are mainly alpha helix. The definition of a structurally more conserved core may be useful in model building proteins from an homologous family. The RMS differences of coordinates of structures of proteins with identical sequences are found to be related to the resolutions of the structures.
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Affiliation(s)
- T J Hubbard
- Department of Crystallography, Birkbeck College, University of London, UK
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41
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Abstract
Four major heat-shock proteins (hsps) with apparent molecular masses of 84, 69, 32 and 22 kDa were detected in exponentially growing stationary phase and sporulating cells of Bacillus subtilis heat-shocked from 30 to 43 degrees C. The most abundant, hsp69, is probably analogous to the E. coli groEL protein. These proteins were transiently inducible by heat-shock. Partial purification of RNA polymerase revealed several other minor hsps. One of these, a 48 kDa polypeptide probably corresponds to sigma 43. The synthesis of this polypeptide and at least two other proteins appeared to be under sporulation and heat-shock regulation and was affected by the SpoOA mutation.
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42
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Mullally DI, Howard WA, Hubbard TJ, Grauman JS, Cohen SG. Increased hospitalizations for asthma among children in the Washington, D.C. area during 1961-1981. Ann Allergy 1984; 53:15-19. [PMID: 6742520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Hospital admissions for childhood asthma to three university affiliated hospitals in the Washington D.C. area (Children's Hospital National Medical Center, CHNMC, Prince George's General Hospital, PGGH, and Holy Cross Hospital, HCH) for the period 1961-1981 increased at least three to 18 fold. The over-all population of children less than or equal to 14 years of age increased, at most, only 1.5 fold by 1970, and thereafter decreased gradually until the end of the study. This increase in pediatric asthma hospitalizations has occurred despite significant improvements in the ambulatory management of the asthmatic child. In particular, the amount of specific anti-asthmatic medication prescribed for these patients has grown markedly. The increased hospitalization is most likely due to an increase in the occurrence of severe asthma in children, particularly black children.
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