1
|
Ravenstijn M, Jansen RC, du Bois G, Yzer S, Klaver CCW. Empowering patients with high myopia: The significance of education. Acta Ophthalmol 2024; 102:357-363. [PMID: 37899508 DOI: 10.1111/aos.15779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/01/2023] [Accepted: 09/18/2023] [Indexed: 10/31/2023]
Abstract
PURPOSE To investigate the status of patient education among highly myopic individuals focusing on the presence, sources, content, timing of the education and impact on patients. METHODS Self-reported data were collected through an online 13-item questionnaire consisting of open and multiple-choice questions. The questionnaire was sent to 250 highly myopic members of a patient organization in the Netherlands, of whom 128 (51%) responded. RESULTS At least one acute event had occurred in 66% (84/128) of participants at the time of the questionnaire. Among all participants, 25% (32/128) had not received patient education regarding alarm symptoms for any of these events. Among those who had been informed, the ophthalmologist was the most frequent (57%, 73/128) source of information. Participants who visited the ophthalmologist annually were more frequently informed than participants without annual visits (53%, 26/49 versus 26%, 9/35, p = 0.002). Those not informed were more likely to have a more than 3 days patient delay (92%, 12/13). Doctors delay was also present; 26% (22/84) of the participants with alarm symptoms had to wait 2 or more days before the first appointment. Long-term consequences of myopia had been discussed with 102 participants (80%, 102/128), again with the ophthalmologist as the most frequent source (59%, 76/128). PERSPECTIVES Many myopic individuals have not been educated about their increased risk of acute events, which can result in patient delay and serious consequences with respect to visual prognosis. These findings underscore the critical importance of integrating patient education across the entire ophthalmic care chain for myopia.
Collapse
Affiliation(s)
- M Ravenstijn
- Rotterdam Ophthalmic Institute, Rotterdam Eye Hospital, Rotterdam, The Netherlands
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - R C Jansen
- Oogvereniging, Utrecht, The Netherlands
- Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands
| | - G du Bois
- Oogvereniging, Utrecht, The Netherlands
| | - S Yzer
- Department of Ophthalmology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - C C W Klaver
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Ophthalmology, Radboud University Medical Centre, Nijmegen, The Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Institute of Molecular and Clinical Ophthalmology, University of Basel, Basel, Switzerland
| |
Collapse
|
2
|
Ravenstijn M, du Bois G, Jansen RC, Liu C, Luyten GPM, van Leeuwen R, Dickman MM, Reus NJ, Yzer S, Klaver CCW. A view from the clinic - Perspectives from Dutch patients and professionals on high myopia care. Ophthalmic Physiol Opt 2023; 43:327-336. [PMID: 36648005 DOI: 10.1111/opo.13091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/21/2022] [Accepted: 12/29/2022] [Indexed: 01/18/2023]
Abstract
PURPOSE To understand and compare perspectives of patients and professionals on current ophthalmologic care for high myopia, and to identify challenges and future opportunities. METHODS Self-reported data were collected through two online questionnaires. Patient perspective was obtained from highly myopic members of a patient organisation based in the Netherlands using a 17-item questionnaire consisting of open and multiple-choice questions regarding personal experience with myopia care. The ophthalmologist perspective was obtained from practising Dutch ophthalmologists with a 12-item questionnaire of multiple-choice questions on work-related demographics, myopia care in daily practice and need for improvement. The response rate for patients was 27% (n = 136/500) and for ophthalmologists, 24% (n = 169/716). RESULTS Patients were highly concerned about personal progressive loss of vision (69%) and feared their psychological well-being (82%) in case this would happen. The quality of performance of care provided by ophthalmologists was rated as excellent or satisfactory by 64% of the patients. These ratings for multidisciplinary care and insurance reimbursement were as low as 28% and 18% respectively. The mean concern among ophthalmologists about the rise in high myopia was 6.9 (SEM 0.1) on a 10-point scale. Sixty-nine per cent of the ophthalmologists reported that asymptomatic myopic patients should not be examined regularly at outpatient clinics. Ophthalmologists urged the development of clinical guidelines (74%), but did report (95%) that they informed patients about risk factors and complications. This contrasted with the view of patients, of whom 42% were discontent with information provided by ophthalmologists. CONCLUSIONS These questionnaires demonstrated that the current clinical care delivered to highly myopic patients is in need of improvement. The expected higher demand for myopia care in the near future requires preferred practice patterns, professionals specifically trained to manage myopic pathology, accurate and comprehensive information exchange and collaboration of in- and out-of-hospital professionals across the full eye care chain.
Collapse
Affiliation(s)
- Monica Ravenstijn
- Rotterdam Ophthalmic Institute, the Rotterdam Eye Hospital, Rotterdam, the Netherlands.,Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | - Ritsert C Jansen
- Oogvereniging, Utrecht, the Netherlands.,Groningen Bioinformatics Centre, University of Groningen, Groningen, the Netherlands
| | - Chang Liu
- Rotterdam Ophthalmic Institute, the Rotterdam Eye Hospital, Rotterdam, the Netherlands
| | - Gregorius P M Luyten
- Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands
| | - Redmer van Leeuwen
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Mor M Dickman
- University Eye Clinic Maastricht, Maastricht University Medical Center, Maastricht, the Netherlands.,MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, the Netherlands
| | - Nic J Reus
- Department of Ophthalmology, Amphia Hospital, Breda, the Netherlands
| | - Suzanne Yzer
- Department of Ophthalmology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, the Netherlands.,Department of Ophthalmology, Radboud University Medical Centre, Nijmegen, the Netherlands.,Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands.,Institute of Molecular and Clinical Ophthalmology, University of Basel, Basel, Switzerland
| |
Collapse
|
3
|
Zych K, Gort G, Maliepaard CA, Jansen RC, Voorrips RE. FitTetra 2.0 - improved genotype calling for tetraploids with multiple population and parental data support. BMC Bioinformatics 2019; 20:148. [PMID: 30894135 PMCID: PMC6425654 DOI: 10.1186/s12859-019-2703-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 02/26/2019] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Genetic studies in tetraploids are lagging behind in comparison with studies of diploids as the complex genetics of tetraploids require much more elaborated computational methodologies. Recent advancements in development of molecular techniques and computational tools facilitate new methods for automated, high-throughput genotype calling in tetraploid species. We report on the upgrade of the widely-used fitTetra software aiming to improve its accuracy, which to date is hampered by technical artefacts in the data. RESULTS Our upgrade of the fitTetra package is designed for a more accurate modelling of complex collections of samples. The package fits a mixture model where some parameters of the model are estimated separately for each sub-collection. When a full-sib family is analyzed, we use parental genotypes to predict the expected segregation in terms of allele dosages in the offspring. More accurate modelling and use of parental data increases the accuracy of dosage calling. We tested the package on data obtained with an Affymetrix Axiom 60 k array and compared its performance with the original version and the recently published ClusterCall tool, showing that at least 20% more SNPs could be called with our updated. CONCLUSION Our updated software package shows clearly improved performance in genotype calling accuracy. Estimation of mixing proportions of the underlying dosage distributions is separated for full-sib families (where mixture proportions can be estimated from the parental dosages and inheritance model) and unstructured populations (where they are based on the assumption of Hardy-Weinberg equilibrium). Additionally, as the distributions of signal ratios of the dosage classes can be assumed to be the same for all populations, including parental data for some subpopulations helps to improve fitting other populations as well. The R package fitTetra 2.0 is freely available under the GNU Public License as Additional file with this article.
Collapse
Affiliation(s)
- Konrad Zych
- Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands
| | - Gerrit Gort
- Wageningen University and Research - Biometris, Wageningen, The Netherlands
| | - Chris A Maliepaard
- Wageningen University and Research - Plant Breeding, Wageningen, The Netherlands
| | - Ritsert C Jansen
- Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands
| | - Roeland E Voorrips
- Wageningen University and Research - Plant Breeding, Wageningen, The Netherlands.
| |
Collapse
|
4
|
Zych K, Snoek BL, Elvin M, Rodriguez M, Van der Velde KJ, Arends D, Westra HJ, Swertz MA, Poulin G, Kammenga JE, Breitling R, Jansen RC, Li Y. reGenotyper: Detecting mislabeled samples in genetic data. PLoS One 2017; 12:e0171324. [PMID: 28192439 PMCID: PMC5305221 DOI: 10.1371/journal.pone.0171324] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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: 07/22/2016] [Accepted: 01/19/2017] [Indexed: 12/11/2022] Open
Abstract
In high-throughput molecular profiling studies, genotype labels can be wrongly assigned at various experimental steps; the resulting mislabeled samples seriously reduce the power to detect the genetic basis of phenotypic variation. We have developed an approach to detect potential mislabeling, recover the “ideal” genotype and identify “best-matched” labels for mislabeled samples. On average, we identified 4% of samples as mislabeled in eight published datasets, highlighting the necessity of applying a “data cleaning” step before standard data analysis.
Collapse
Affiliation(s)
- Konrad Zych
- Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands
| | - Basten L. Snoek
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| | - Mark Elvin
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Miriam Rodriguez
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| | - K. Joeri Van der Velde
- Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Danny Arends
- Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands
| | - Harm-Jan Westra
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Partners Center for Personalized Genetic Medicine, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Morris A. Swertz
- Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Gino Poulin
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Jan E. Kammenga
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| | - Rainer Breitling
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Ritsert C. Jansen
- Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands
| | - Yang Li
- Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
- * E-mail:
| |
Collapse
|
5
|
Zych K, Li Y, van der Velde JK, Joosen RVL, Ligterink W, Jansen RC, Arends D. Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains. BMC Bioinformatics 2015; 16:51. [PMID: 25886992 PMCID: PMC4339742 DOI: 10.1186/s12859-015-0475-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [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: 10/22/2014] [Accepted: 01/26/2015] [Indexed: 11/11/2022] Open
Abstract
Background Genetic markers and maps are instrumental in quantitative trait locus (QTL) mapping in segregating populations. The resolution of QTL localization depends on the number of informative recombinations in the population and how well they are tagged by markers. Larger populations and denser marker maps are better for detecting and locating QTLs. Marker maps that are initially too sparse can be saturated or derived de novo from high-throughput omics data, (e.g. gene expression, protein or metabolite abundance). If these molecular phenotypes are affected by genetic variation due to a major QTL they will show a clear multimodal distribution. Using this information, phenotypes can be converted into genetic markers. Results The Pheno2Geno tool uses mixture modeling to select phenotypes and transform them into genetic markers suitable for construction and/or saturation of a genetic map. Pheno2Geno excludes candidate genetic markers that show evidence for multiple possibly epistatically interacting QTL and/or interaction with the environment, in order to provide a set of robust markers for follow-up QTL mapping. We demonstrate the use of Pheno2Geno on gene expression data of 370,000 probes in 148 A. thaliana recombinant inbred lines. Pheno2Geno is able to saturate the existing genetic map, decreasing the average distance between markers from 7.1 cM to 0.89 cM, close to the theoretical limit of 0.68 cM (with 148 individuals we expect a recombination every 100/148=0.68 cM); this pinpointed almost all of the informative recombinations in the population. Conclusion The Pheno2Geno package makes use of genome-wide molecular profiling and provides a tool for high-throughput de novo map construction and saturation of existing genetic maps. Processing of the showcase dataset takes less than 30 minutes on an average desktop PC. Pheno2Geno improves QTL mapping results at no additional laboratory cost and with minimum computational effort. Its results are formatted for direct use in R/qtl, the leading R package for QTL studies. Pheno2Geno is freely available on CRAN under “GNU GPL v3”. The Pheno2Geno package as well as the tutorial can also be found at: http://pheno2geno.nl. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0475-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Konrad Zych
- University of Groningen, Groningen Bioinformatics Centre, Nijenborgh 7, Groningen, 9747, AG, The Netherlands. .,Jagiellonian University, Faculty of Biochemistry, Biophysics and Biotechnology, Gronostajowa Street 7, Krakow, 30-387, Poland.
| | - Yang Li
- University of Groningen, Groningen Bioinformatics Centre, Nijenborgh 7, Groningen, 9747, AG, The Netherlands. .,University of Groningen, University Medical Center Groningen, Department of Genetics, PO Box 30001, Groningen, 9700, RB, The Netherlands.
| | - Joeri K van der Velde
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, PO Box 30001, Groningen, 9700, RB, The Netherlands.
| | - Ronny V L Joosen
- Wageningen University, Wageningen Seed Lab, Droevendaalsesteeg 1, Wageningen, The Netherlands.
| | - Wilco Ligterink
- Wageningen University, Wageningen Seed Lab, Droevendaalsesteeg 1, Wageningen, The Netherlands.
| | - Ritsert C Jansen
- University of Groningen, Groningen Bioinformatics Centre, Nijenborgh 7, Groningen, 9747, AG, The Netherlands.
| | - Danny Arends
- University of Groningen, Groningen Bioinformatics Centre, Nijenborgh 7, Groningen, 9747, AG, The Netherlands.
| |
Collapse
|
6
|
Fehrmann RSN, Karjalainen JM, Krajewska M, Westra HJ, Maloney D, Simeonov A, Pers TH, Hirschhorn JN, Jansen RC, Schultes EA, van Haagen HHHBM, de Vries EGE, te Meerman GJ, Wijmenga C, van Vugt MATM, Franke L. Gene expression analysis identifies global gene dosage sensitivity in cancer. Nat Genet 2015; 47:115-25. [PMID: 25581432 DOI: 10.1038/ng.3173] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 12/02/2014] [Indexed: 12/13/2022]
Abstract
Many cancer-associated somatic copy number alterations (SCNAs) are known. Currently, one of the challenges is to identify the molecular downstream effects of these variants. Although several SCNAs are known to change gene expression levels, it is not clear whether each individual SCNA affects gene expression. We reanalyzed 77,840 expression profiles and observed a limited set of 'transcriptional components' that describe well-known biology, explain the vast majority of variation in gene expression and enable us to predict the biological function of genes. On correcting expression profiles for these components, we observed that the residual expression levels (in 'functional genomic mRNA' profiling) correlated strongly with copy number. DNA copy number correlated positively with expression levels for 99% of all abundantly expressed human genes, indicating global gene dosage sensitivity. By applying this method to 16,172 patient-derived tumor samples, we replicated many loci with aberrant copy numbers and identified recurrently disrupted genes in genomically unstable cancers.
Collapse
Affiliation(s)
- Rudolf S N Fehrmann
- 1] Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands. [2] Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Juha M Karjalainen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Małgorzata Krajewska
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Harm-Jan Westra
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - David Maloney
- National Center for Advancing Translational Sciences, US National Institutes of Health, Rockville, Maryland, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, US National Institutes of Health, Rockville, Maryland, USA
| | - Tune H Pers
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Division of Endocrinology, Children's Hospital Boston, Boston, Massachusetts, USA. [3] Center for Basic and Translational Obesity Research, Children's Hospital Boston, Boston, Massachusetts, USA. [4] Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Joel N Hirschhorn
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Division of Endocrinology, Children's Hospital Boston, Boston, Massachusetts, USA. [3] Center for Basic and Translational Obesity Research, Children's Hospital Boston, Boston, Massachusetts, USA. [4] Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Ritsert C Jansen
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, the Netherlands
| | - Erik A Schultes
- 1] Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands. [2] BioSemantics Group, Leiden Institute of Advanced Computer Science, Leiden University, Leiden, the Netherlands
| | | | - Elisabeth G E de Vries
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Gerard J te Meerman
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marcel A T M van Vugt
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| |
Collapse
|
7
|
Rintisch C, Heinig M, Bauerfeind A, Schafer S, Mieth C, Patone G, Hummel O, Chen W, Cook S, Cuppen E, Colomé-Tatché M, Johannes F, Jansen RC, Neil H, Werner M, Pravenec M, Vingron M, Hubner N. Natural variation of histone modification and its impact on gene expression in the rat genome. Genome Res 2014; 24:942-53. [PMID: 24793478 PMCID: PMC4032858 DOI: 10.1101/gr.169029.113] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [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: 11/25/2022]
Abstract
Histone modifications are epigenetic marks that play fundamental roles in many biological processes including the control of chromatin-mediated regulation of gene expression. Little is known about interindividual variability of histone modification levels across the genome and to what extent they are influenced by genetic variation. We annotated the rat genome with histone modification maps, identified differences in histone trimethyl-lysine levels among strains, and described their underlying genetic basis at the genome-wide scale using ChIP-seq in heart and liver tissues in a panel of rat recombinant inbred and their progenitor strains. We identified extensive variation of histone methylation levels among individuals and mapped hundreds of underlying cis- and trans-acting loci throughout the genome that regulate histone methylation levels in an allele-specific manner. Interestingly, most histone methylation level variation was trans-linked and the most prominent QTL identified influenced H3K4me3 levels at 899 putative promoters throughout the genome in the heart. Cis- acting variation was enriched in binding sites of distinct transcription factors in heart and liver. The integrated analysis of DNA variation together with histone methylation and gene expression levels showed that histoneQTLs are an important predictor of gene expression and that a joint analysis significantly enhanced the prediction of gene expression traits (eQTLs). Our data suggest that genetic variation has a widespread impact on histone trimethylation marks that may help to uncover novel genotype-phenotype relationships.
Collapse
Affiliation(s)
- Carola Rintisch
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Matthias Heinig
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany; Department of Computational Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Anja Bauerfeind
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Sebastian Schafer
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Christin Mieth
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Giannino Patone
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Oliver Hummel
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Wei Chen
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Stuart Cook
- National Heart and Lung Institute, Cardiovascular Genetics and Genomics, London, SW3 6NP, United Kingdom; Duke-NUS Graduate Medical School, 169857 Singapore; National Heart Center Singapore, 169609 Singapore
| | - Edwin Cuppen
- Center for Molecular Medicine, University Medical Center Utrecht, Hubrecht Institute KNAW, 3584 CT Utrecht, The Netherlands
| | - Maria Colomé-Tatché
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, NL-9713 AV Groningen, The Netherlands
| | - Frank Johannes
- Groningen Bioinformatics Centre (GBIC), Groningen Biomolecular Sciences and Biotechnology Institute (GBB), 9747AG Groningen, The Netherlands
| | - Ritsert C Jansen
- Groningen Bioinformatics Centre (GBIC), Groningen Biomolecular Sciences and Biotechnology Institute (GBB), 9747AG Groningen, The Netherlands
| | - Helen Neil
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), iBiTec-S, Université Paris-Sud, CNRS FRE3377, F-91191 Gif-sur-Yvette cedex, France
| | - Michel Werner
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), iBiTec-S, Université Paris-Sud, CNRS FRE3377, F-91191 Gif-sur-Yvette cedex, France
| | - Michal Pravenec
- Institut of Physiology, Academy of Sciences of the Czech Republic, Videnska 1083, CZ-14220 Prague 4, Czech Republic
| | - Martin Vingron
- Department of Computational Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Norbert Hubner
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner site Berlin, 13125 Berlin, Germany
| |
Collapse
|
8
|
Snoek LB, Joeri van der Velde K, Li Y, Jansen RC, Swertz MA, Kammenga JE. Worm variation made accessible: Take your shopping cart to store, link, and investigate! Worm 2014; 3:e28357. [PMID: 24843834 PMCID: PMC4024057 DOI: 10.4161/worm.28357] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 02/17/2014] [Accepted: 02/25/2014] [Indexed: 11/20/2022]
Abstract
In Caenorhabditis elegans, the recent advances in high-throughput quantitative analyses of natural genetic and phenotypic variation have led to a wealth of data on genotype phenotype relations. This data has resulted in the discovery of genes with major allelic effects and insights in the effect of natural genetic variation on a whole range of complex traits as well as how this variation is distributed across the genome. Regardless of the advances presented in specific studies, the majority of the data generated in these studies had yet to be made easily accessible, allowing for meta-analysis. Not only data in figures or tables but meta-data should be accessible for further investigation and comparison between studies. A platform was created where all the data, phenotypic measurements, genotypes, and mappings can be stored, compared, and new linkages within and between published studies can be discovered. WormQTL focuses on quantitative genetics in Caenorhabditis and other nematode species, whereas WormQTLHD quantitatively links gene expression quantitative trait loci (eQTL) in C. elegans to gene–disease associations in humans.
Collapse
Affiliation(s)
- L Basten Snoek
- Laboratory of Nematology; Wageningen University; The Netherlands
| | - K Joeri van der Velde
- Genomics Coordination Center; University of Groningen; University Medical Center Groningen; The Netherlands ; Groningen Bioinformatics Center; University of Groningen; The Netherlands ; Department of Genetics; University of Groningen; University Medical Center Groningen; The Netherlands
| | - Yang Li
- Genomics Coordination Center; University of Groningen; University Medical Center Groningen; The Netherlands ; Groningen Bioinformatics Center; University of Groningen; The Netherlands
| | - Ritsert C Jansen
- Groningen Bioinformatics Center; University of Groningen; The Netherlands
| | - Morris A Swertz
- Genomics Coordination Center; University of Groningen; University Medical Center Groningen; The Netherlands ; Groningen Bioinformatics Center; University of Groningen; The Netherlands ; Department of Genetics; University of Groningen; University Medical Center Groningen; The Netherlands
| | - Jan E Kammenga
- Laboratory of Nematology; Wageningen University; The Netherlands
| |
Collapse
|
9
|
van der Velde KJ, de Haan M, Zych K, Arends D, Snoek LB, Kammenga JE, Jansen RC, Swertz MA, Li Y. WormQTLHD--a web database for linking human disease to natural variation data in C. elegans. Nucleic Acids Res 2013; 42:D794-801. [PMID: 24217915 PMCID: PMC3965109 DOI: 10.1093/nar/gkt1044] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [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
Interactions between proteins are highly conserved across species. As a result, the molecular basis of multiple diseases affecting humans can be studied in model organisms that offer many alternative experimental opportunities. One such organism—Caenorhabditis elegans—has been used to produce much molecular quantitative genetics and systems biology data over the past decade. We present WormQTLHD (Human Disease), a database that quantitatively and systematically links expression Quantitative Trait Loci (eQTL) findings in C. elegans to gene–disease associations in man. WormQTLHD, available online at http://www.wormqtl-hd.org, is a user-friendly set of tools to reveal functionally coherent, evolutionary conserved gene networks. These can be used to predict novel gene-to-gene associations and the functions of genes underlying the disease of interest. We created a new database that links C. elegans eQTL data sets to human diseases (34 337 gene–disease associations from OMIM, DGA, GWAS Central and NHGRI GWAS Catalogue) based on overlapping sets of orthologous genes associated to phenotypes in these two species. We utilized QTL results, high-throughput molecular phenotypes, classical phenotypes and genotype data covering different developmental stages and environments from WormQTL database. All software is available as open source, built on MOLGENIS and xQTL workbench.
Collapse
Affiliation(s)
- K Joeri van der Velde
- Genomics Coordination Center, University of Groningen, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen, The Netherlands, Groningen Bioinformatics Center, University of Groningen, P.O. Box 11103, 9700 CC Groningen, The Netherlands, Department of Genetics, University of Groningen, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen, The Netherlands, Department of Bioinformatics, Hanze University of Applied Sciences, Groningen, Zernikeplein 11, 9747 AS, The Netherlands and Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Joosen RVL, Arends D, Li Y, Willems LA, Keurentjes JJ, Ligterink W, Jansen RC, Hilhorst HW. Identifying genotype-by-environment interactions in the metabolism of germinating arabidopsis seeds using generalized genetical genomics. Plant Physiol 2013; 162:553-66. [PMID: 23606598 PMCID: PMC3668052 DOI: 10.1104/pp.113.216176] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 04/17/2013] [Indexed: 05/18/2023]
Abstract
A complex phenotype such as seed germination is the result of several genetic and environmental cues and requires the concerted action of many genes. The use of well-structured recombinant inbred lines in combination with "omics" analysis can help to disentangle the genetic basis of such quantitative traits. This so-called genetical genomics approach can effectively capture both genetic and epistatic interactions. However, to understand how the environment interacts with genomic-encoded information, a better understanding of the perception and processing of environmental signals is needed. In a classical genetical genomics setup, this requires replication of the whole experiment in different environmental conditions. A novel generalized setup overcomes this limitation and includes environmental perturbation within a single experimental design. We developed a dedicated quantitative trait loci mapping procedure to implement this approach and used existing phenotypical data to demonstrate its power. In addition, we studied the genetic regulation of primary metabolism in dry and imbibed Arabidopsis (Arabidopsis thaliana) seeds. In the metabolome, many changes were observed that were under both environmental and genetic controls and their interaction. This concept offers unique reduction of experimental load with minimal compromise of statistical power and is of great potential in the field of systems genetics, which requires a broad understanding of both plasticity and dynamic regulation.
Collapse
|
11
|
Snoek LB, Van der Velde KJ, Arends D, Li Y, Beyer A, Elvin M, Fisher J, Hajnal A, Hengartner MO, Poulin GB, Rodriguez M, Schmid T, Schrimpf S, Xue F, Jansen RC, Kammenga JE, Swertz MA. WormQTL--public archive and analysis web portal for natural variation data in Caenorhabditis spp. Nucleic Acids Res 2012. [PMID: 23180786 PMCID: PMC3531126 DOI: 10.1093/nar/gks1124] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [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: 12/11/2022] Open
Abstract
Here, we present WormQTL (http://www.wormqtl.org), an easily accessible database enabling search, comparative analysis and meta-analysis of all data on variation in Caenorhabditis spp. Over the past decade, Caenorhabditis elegans has become instrumental for molecular quantitative genetics and the systems biology of natural variation. These efforts have resulted in a valuable amount of phenotypic, high-throughput molecular and genotypic data across different developmental worm stages and environments in hundreds of C. elegans strains. WormQTL provides a workbench of analysis tools for genotype-phenotype linkage and association mapping based on but not limited to R/qtl (http://www.rqtl.org). All data can be uploaded and downloaded using simple delimited text or Excel formats and are accessible via a public web user interface for biologists and R statistic and web service interfaces for bioinformaticians, based on open source MOLGENIS and xQTL workbench software. WormQTL welcomes data submissions from other worm researchers.
Collapse
Affiliation(s)
- L Basten Snoek
- Laboratory of Nematology, Wageningen University, Wageningen 6708 PB, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Lendvai Á, Johannes F, Grimm C, Eijsink JJH, Wardenaar R, Volders HH, Klip HG, Hollema H, Jansen RC, Schuuring E, Wisman GBA, van der Zee AGJ. Genome-wide methylation profiling identifies hypermethylated biomarkers in high-grade cervical intraepithelial neoplasia. Epigenetics 2012; 7:1268-78. [PMID: 23018867 DOI: 10.4161/epi.22301] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Epigenetic modifications, such as aberrant DNA promoter methylation, are frequently observed in cervical cancer. Identification of hypermethylated regions allowing discrimination between normal cervical epithelium and high-grade cervical intraepithelial neoplasia (CIN2/3), or worse, may improve current cervical cancer population-based screening programs. In this study, the DNA methylome of high-grade CIN lesions was studied using genome-wide DNA methylation screening to identify potential biomarkers for early diagnosis of cervical neoplasia. Methylated DNA Immunoprecipitation (MeDIP) combined with DNA microarray was used to compare DNA methylation profiles of epithelial cells derived from high-grade CIN lesions with normal cervical epithelium. Hypermethylated differentially methylated regions (DMRs) were identified. Validation of nine selected DMRs using BSP and MSP in cervical tissue revealed methylation in 63.2-94.7% high-grade CIN and in 59.3-100% cervical carcinomas. QMSP for the two most significant high-grade CIN-specific methylation markers was conducted exploring test performance in a large series of cervical scrapings. Frequency and relative level of methylation were significantly different between normal and cancer samples. Clinical validation of both markers in cervical scrapings from patients with an abnormal cervical smear confirmed that frequency and relative level of methylation were related with increasing severity of the underlying CIN lesion and that ROC analysis was discriminative. These markers represent the COL25A1 and KATNAL2 and their observed increased methylation upon progression could intimate the regulatory role in carcinogenesis. In conclusion, our newly identified hypermethylated DMRs represent specific DNA methylation patterns in high-grade CIN lesions and are candidate biomarkers for early detection.
Collapse
Affiliation(s)
- Ágnes Lendvai
- Department of Gynaecological Oncology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Lendvai A, Johannes F, Grimm C, Eijsink JJH, Wardenaar R, Volders HH, Klip HG, Hollema H, Jansen RC, Schuuring E, van der Zee AGJ, Wisman GBA. Abstract 5011: Genome-wide methylation profiling identifies hypermethylated biomarkers in high-grade cervical intraepithelial neoplasia. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-5011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Cervical cancer is the second most common cancer in women worldwide and development of cervical cancer goes through different well-defined premalignant stages. Epigenetic modifications, such as aberrant DNA promoter methylation is frequently observed in cervical cancer. Identification of hypermethylated regions that allow discrimination between normal cervical epithelium and high-grade cervical intraepithelial neoplasia or worse (CIN2+) by DNA methylation state may improve current population-based screening programs for cervical cancer. In this study, the DNA methylome of CIN3 lesions were characterized using genome-wide methylation screening to identify potential biomarkers for early diagnosis of cervical neoplasia. Methods and results: Methyl-DNA ImmunoPrecipitation (MeDIP) assay combined with DNA microarray hybridization was used to compare DNA methylation patterns of epithelial cells derived from CIN3 lesions with normal cervical epithelium. In total, 80 hypermethylated differentially methylated regions (DMRs) were identified that significantly distinguished CIN3 lesions from normal cervice. Selected DMRs (n=9) were evaluated by methylation-specific PCR (MSP) on additional tissue specimens including normal cervix, CIN2/3 and cervical cancer samples and showed hypermethylation in up to 94.7% in CIN2/3 and 100% in cervical cancers. Quantitative MSP (QMSP) for two candidate biomarkers was applied to explore the test performance in a large series of cervical scrapings. Frequency and relative level of DNA methylation were significantly different between normal and cancer samples (p<0.05). In cervical scrapings from patients referred with an abnormal Pap smear, frequency and relative level of DNA methylation were also related with increasing severity of the underlying CIN lesion (p<0.01) In addition, ROC analysis showed that the methylation level was discriminative between low-grade CIN lesions and CIN2+ (p<0.05). Conclusion: Our study demonstrates specific DNA methylation patterns in high-grade CIN lesions through the newly identified discriminative hypermethylated DMRs and represents candidate biomarkers for early detection of high-grade CIN. This study was supported by the Dutch Cancer Society (NKB) (project-number RUG 2004-3161) and by OncoMethylome Sciences S.A., Liège, Belgium. CG was funded by the German Ministry of Education and Research (BMBF) within the NGFN-PLUS project PKT-01GS08111.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5011. doi:1538-7445.AM2012-5011
Collapse
Affiliation(s)
- Agnes Lendvai
- 1Univ. Medical Ctr. Groningen, Groningen, Netherlands
| | | | - Christina Grimm
- 3Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | | | | | - Harry G. Klip
- 1Univ. Medical Ctr. Groningen, Groningen, Netherlands
| | - Harry Hollema
- 1Univ. Medical Ctr. Groningen, Groningen, Netherlands
| | | | - Ed Schuuring
- 1Univ. Medical Ctr. Groningen, Groningen, Netherlands
| | | | | |
Collapse
|
14
|
Diekstra FP, Saris CGJ, van Rheenen W, Franke L, Jansen RC, van Es MA, van Vught PWJ, Blauw HM, Groen EJN, Horvath S, Estrada K, Rivadeneira F, Hofman A, Uitterlinden AG, Robberecht W, Andersen PM, Melki J, Meininger V, Hardiman O, Landers JE, Brown RH, Shatunov A, Shaw CE, Leigh PN, Al-Chalabi A, Ophoff RA, van den Berg LH, Veldink JH. Mapping of gene expression reveals CYP27A1 as a susceptibility gene for sporadic ALS. PLoS One 2012; 7:e35333. [PMID: 22509407 PMCID: PMC3324559 DOI: 10.1371/journal.pone.0035333] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [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: 12/20/2011] [Accepted: 03/13/2012] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive, neurodegenerative disease characterized by loss of upper and lower motor neurons. ALS is considered to be a complex trait and genome-wide association studies (GWAS) have implicated a few susceptibility loci. However, many more causal loci remain to be discovered. Since it has been shown that genetic variants associated with complex traits are more likely to be eQTLs than frequency-matched variants from GWAS platforms, we conducted a two-stage genome-wide screening for eQTLs associated with ALS. In addition, we applied an eQTL analysis to finemap association loci. Expression profiles using peripheral blood of 323 sporadic ALS patients and 413 controls were mapped to genome-wide genotyping data. Subsequently, data from a two-stage GWAS (3,568 patients and 10,163 controls) were used to prioritize eQTLs identified in the first stage (162 ALS, 207 controls). These prioritized eQTLs were carried forward to the second sample with both gene-expression and genotyping data (161 ALS, 206 controls). Replicated eQTL SNPs were then tested for association in the second-stage GWAS data to find SNPs associated with disease, that survived correction for multiple testing. We thus identified twelve cis eQTLs with nominally significant associations in the second-stage GWAS data. Eight SNP-transcript pairs of highest significance (lowest p = 1.27×10−51) withstood multiple-testing correction in the second stage and modulated CYP27A1 gene expression. Additionally, we show that C9orf72 appears to be the only gene in the 9p21.2 locus that is regulated in cis, showing the potential of this approach in identifying causative genes in association loci in ALS. This study has identified candidate genes for sporadic ALS, most notably CYP27A1. Mutations in CYP27A1 are causal to cerebrotendinous xanthomatosis which can present as a clinical mimic of ALS with progressive upper motor neuron loss, making it a plausible susceptibility gene for ALS.
Collapse
Affiliation(s)
- Frank P. Diekstra
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Christiaan G. J. Saris
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Wouter van Rheenen
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Ritsert C. Jansen
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
| | - Michael A. van Es
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Paul W. J. van Vught
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hylke M. Blauw
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ewout J. N. Groen
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Karol Estrada
- Department of Epidemiology and Biostatistics, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Fernando Rivadeneira
- Department of Epidemiology and Biostatistics, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Albert Hofman
- Department of Epidemiology and Biostatistics, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Andre G. Uitterlinden
- Department of Epidemiology and Biostatistics, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Wim Robberecht
- Department of Neurology, University Hospital Leuven, University of Leuven, Leuven, Belgium
- Laboratory for Neurobiology, Vesalius Research Centre, Flanders Institute for Biotechnology (VIB), Leuven, Belgium
| | | | - Judith Melki
- Department of Neuropediatrics, University of Paris, Bicetre Hospital, Paris, France
| | - Vincent Meininger
- Department of Neurology, Université Pierre et Marie Curie, Hôpital de la Salpêtrière, Paris, France
| | - Orla Hardiman
- Department of Neurology, Beaumont Hospital, Dublin, Ireland
- Department of Neurology, Trinity College, Dublin, Ireland
| | - John E. Landers
- Department of Neurology, University of Massachusetts School of Medicine, Worcester, Massachusetts, United States of America
- Department of Neurology, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
| | - Robert H. Brown
- Department of Neurology, University of Massachusetts School of Medicine, Worcester, Massachusetts, United States of America
- Department of Neurology, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
| | - Aleksey Shatunov
- Medical Research Council Centre for Neurodegeneration Research, King’s College London, Department of Clinical Neuroscience, Institute of Psychiatry, London, United Kingdom
| | - Christopher E. Shaw
- Medical Research Council Centre for Neurodegeneration Research, King’s College London, Department of Clinical Neuroscience, Institute of Psychiatry, London, United Kingdom
| | - P. Nigel Leigh
- Medical Research Council Centre for Neurodegeneration Research, King’s College London, Department of Clinical Neuroscience, Institute of Psychiatry, London, United Kingdom
| | - Ammar Al-Chalabi
- Medical Research Council Centre for Neurodegeneration Research, King’s College London, Department of Clinical Neuroscience, Institute of Psychiatry, London, United Kingdom
| | - Roel A. Ophoff
- Department of Medical Genetics, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
- Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Leonard H. van den Berg
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jan H. Veldink
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
- * E-mail:
| |
Collapse
|
15
|
Demirkan A, van Duijn CM, Ugocsai P, Isaacs A, Pramstaller PP, Liebisch G, Wilson JF, Johansson Å, Rudan I, Aulchenko YS, Kirichenko AV, Janssens ACJW, Jansen RC, Gnewuch C, Domingues FS, Pattaro C, Wild SH, Jonasson I, Polasek O, Zorkoltseva IV, Hofman A, Karssen LC, Struchalin M, Floyd J, Igl W, Biloglav Z, Broer L, Pfeufer A, Pichler I, Campbell S, Zaboli G, Kolcic I, Rivadeneira F, Huffman J, Hastie ND, Uitterlinden A, Franke L, Franklin CS, Vitart V, Nelson CP, Preuss M, Bis JC, O'Donnell CJ, Franceschini N, Witteman JCM, Axenovich T, Oostra BA, Meitinger T, Hicks AA, Hayward C, Wright AF, Gyllensten U, Campbell H, Schmitz G. Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations. PLoS Genet 2012; 8:e1002490. [PMID: 22359512 PMCID: PMC3280968 DOI: 10.1371/journal.pgen.1002490] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [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: 08/05/2011] [Accepted: 12/05/2011] [Indexed: 11/19/2022] Open
Abstract
Phospho- and sphingolipids are crucial cellular and intracellular compounds. These lipids are required for active transport, a number of enzymatic processes, membrane formation, and cell signalling. Disruption of their metabolism leads to several diseases, with diverse neurological, psychiatric, and metabolic consequences. A large number of phospholipid and sphingolipid species can be detected and measured in human plasma. We conducted a meta-analysis of five European family-based genome-wide association studies (N = 4034) on plasma levels of 24 sphingomyelins (SPM), 9 ceramides (CER), 57 phosphatidylcholines (PC), 20 lysophosphatidylcholines (LPC), 27 phosphatidylethanolamines (PE), and 16 PE-based plasmalogens (PLPE), as well as their proportions in each major class. This effort yielded 25 genome-wide significant loci for phospholipids (smallest P-value = 9.88×10−204) and 10 loci for sphingolipids (smallest P-value = 3.10×10−57). After a correction for multiple comparisons (P-value<2.2×10−9), we observed four novel loci significantly associated with phospholipids (PAQR9, AGPAT1, PKD2L1, PDXDC1) and two with sphingolipids (PLD2 and APOE) explaining up to 3.1% of the variance. Further analysis of the top findings with respect to within class molar proportions uncovered three additional loci for phospholipids (PNLIPRP2, PCDH20, and ABDH3) suggesting their involvement in either fatty acid elongation/saturation processes or fatty acid specific turnover mechanisms. Among those, 14 loci (KCNH7, AGPAT1, PNLIPRP2, SYT9, FADS1-2-3, DLG2, APOA1, ELOVL2, CDK17, LIPC, PDXDC1, PLD2, LASS4, and APOE) mapped into the glycerophospholipid and 12 loci (ILKAP, ITGA9, AGPAT1, FADS1-2-3, APOA1, PCDH20, LIPC, PDXDC1, SGPP1, APOE, LASS4, and PLD2) to the sphingolipid pathways. In large meta-analyses, associations between FADS1-2-3 and carotid intima media thickness, AGPAT1 and type 2 diabetes, and APOA1 and coronary artery disease were observed. In conclusion, our study identified nine novel phospho- and sphingolipid loci, substantially increasing our knowledge of the genetic basis for these traits. Phospho- and sphingolipids are integral to membrane formation and are involved in crucial cellular functions such as signalling, membrane fluidity, membrane protein trafficking, neurotransmission, and receptor trafficking. In addition to severe monogenic diseases resulting from defective phospho- and sphingolipid function and metabolism, the evidence suggests that variations in these lipid levels at the population level are involved in the determination of cardiovascular and neurologic traits and subsequent disease. We took advantage of modern laboratory methods, including microarray-based genotyping and electrospray ionization tandem mass spectrometry, to hunt for genetic variation influencing the levels of more than 350 phospho- and sphingolipid phenotypes. We identified nine novel loci, in addition to confirming a number of previously described loci. Several other genetic regions provided substantial evidence of their involvement in these traits. All of these loci are strong candidates for further research in the field of lipid biology and are likely to yield considerable insights into the complex metabolic pathways underlying circulating phospho- and sphingolipid levels. Understanding these mechanisms might help to illuminate factors leading to the development of common cardiovascular and neurological diseases and might provide molecular targets for the development of new therapies.
Collapse
Affiliation(s)
- Ayşe Demirkan
- Genetic Epidemiology Unit, Departments of Epidemiology and Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Cornelia M. van Duijn
- Genetic Epidemiology Unit, Departments of Epidemiology and Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
- Centre for Medical Sytems Biology, Leiden, The Netherlands
- Netherlands Consortium for Healthy Aging, Netherlands Genomics Initiative, Leiden, The Netherlands
| | - Peter Ugocsai
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Aaron Isaacs
- Genetic Epidemiology Unit, Departments of Epidemiology and Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
- Centre for Medical Sytems Biology, Leiden, The Netherlands
- * E-mail:
| | - Peter P. Pramstaller
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy
- Department of Neurology, General Central Hospital, Bolzano, Italy
- Department of Neurology, University of Lubeck, Lubeck, Germany
| | - Gerhard Liebisch
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - James F. Wilson
- Centre for Population Health Sciences, The University of Edinburgh Medical School, Edinburgh, United Kingdom
| | - Åsa Johansson
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Igor Rudan
- Centre for Population Health Sciences, The University of Edinburgh Medical School, Edinburgh, United Kingdom
- Institute for Clinical Medical Research, University Hospital “Sestre Milosrdnice”, Zagreb, Croatia
- Croatian Centre for Global Health, Faculty of Medicine, University of Split, Split, Croatia
| | - Yurii S. Aulchenko
- Genetic Epidemiology Unit, Departments of Epidemiology and Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Anatoly V. Kirichenko
- Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | | | - Ritsert C. Jansen
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Carsten Gnewuch
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | | | - Cristian Pattaro
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy
| | - Sarah H. Wild
- Centre for Population Health Sciences, The University of Edinburgh Medical School, Edinburgh, United Kingdom
| | - Inger Jonasson
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
- Croatian Centre for Global Health, Faculty of Medicine, University of Split, Split, Croatia
| | - Ozren Polasek
- Croatian Centre for Global Health, Faculty of Medicine, University of Split, Split, Croatia
| | - Irina V. Zorkoltseva
- Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Albert Hofman
- Netherlands Consortium for Healthy Aging, Netherlands Genomics Initiative, Leiden, The Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lennart C. Karssen
- Genetic Epidemiology Unit, Departments of Epidemiology and Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Maksim Struchalin
- Genetic Epidemiology Unit, Departments of Epidemiology and Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - James Floyd
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Wilmar Igl
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Zrinka Biloglav
- Andrija Stampar School of Public Health, Faculty of Medicine, University of Zagreb, Zagreb, Croatia
| | - Linda Broer
- Genetic Epidemiology Unit, Departments of Epidemiology and Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Arne Pfeufer
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy
| | - Irene Pichler
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy
| | - Susan Campbell
- Centre for Population Health Sciences, The University of Edinburgh Medical School, Edinburgh, United Kingdom
| | - Ghazal Zaboli
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Ivana Kolcic
- Croatian Centre for Global Health, Faculty of Medicine, University of Split, Split, Croatia
| | - Fernando Rivadeneira
- Netherlands Consortium for Healthy Aging, Netherlands Genomics Initiative, Leiden, The Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jennifer Huffman
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Nicholas D. Hastie
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Andre Uitterlinden
- Netherlands Consortium for Healthy Aging, Netherlands Genomics Initiative, Leiden, The Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lude Franke
- Genetics Department, University Medical Centre Groningen and University of Groningen, Groningen, The Netherlands
| | | | - Veronique Vitart
- Centre for Population Health Sciences, The University of Edinburgh Medical School, Edinburgh, United Kingdom
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | | | - Christopher P. Nelson
- Department of Cardiovascular Science, University of Leicester, Leicester, United Kingdom
| | - Michael Preuss
- Institut fur Medizinische Biometrie und Statistik and Medizinische Klinik II, Universitat zu Lubeck, Lubeck, Germany
| | | | - Joshua C. Bis
- Cardiovascular Health Research Unit and Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Christopher J. O'Donnell
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, United States of America
- Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | | | - Jacqueline C. M. Witteman
- Netherlands Consortium for Healthy Aging, Netherlands Genomics Initiative, Leiden, The Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tatiana Axenovich
- Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Ben A. Oostra
- Centre for Medical Sytems Biology, Leiden, The Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Thomas Meitinger
- Institut for Human Genetics, Helmholtz-Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, München, Germany
- Munich Heart Alliance, Munich, Germany
| | - Andrew A. Hicks
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Alan F. Wright
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Ulf Gyllensten
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Harry Campbell
- Centre for Population Health Sciences, The University of Edinburgh Medical School, Edinburgh, United Kingdom
| | - Gerd Schmitz
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | | |
Collapse
|
16
|
Arends D, van der Velde KJ, Prins P, Broman KW, Möller S, Jansen RC, Swertz MA. xQTL workbench: a scalable web environment for multi-level QTL analysis. Bioinformatics 2012; 28:1042-4. [PMID: 22308096 PMCID: PMC3315722 DOI: 10.1093/bioinformatics/bts049] [Citation(s) in RCA: 13] [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] [Indexed: 11/21/2022] Open
Abstract
Summary:xQTL workbench is a scalable web platform for the mapping of quantitative trait loci (QTLs) at multiple levels: for example gene expression (eQTL), protein abundance (pQTL), metabolite abundance (mQTL) and phenotype (phQTL) data. Popular QTL mapping methods for model organism and human populations are accessible via the web user interface. Large calculations scale easily on to multi-core computers, clusters and Cloud. All data involved can be uploaded and queried online: markers, genotypes, microarrays, NGS, LC-MS, GC-MS, NMR, etc. When new data types come available, xQTL workbench is quickly customized using the Molgenis software generator. Availability:xQTL workbench runs on all common platforms, including Linux, Mac OS X and Windows. An online demo system, installation guide, tutorials, software and source code are available under the LGPL3 license from http://www.xqtl.org. Contact:m.a.swertz@rug.nl
Collapse
Affiliation(s)
- Danny Arends
- Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
17
|
Joosen RVL, Arends D, Willems LAJ, Ligterink W, Jansen RC, Hilhorst HW. Visualizing the genetic landscape of Arabidopsis seed performance. Plant Physiol 2012; 158:570-89. [PMID: 22158761 PMCID: PMC3271751 DOI: 10.1104/pp.111.186676] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 12/11/2011] [Indexed: 05/18/2023]
Abstract
Perfect timing of germination is required to encounter optimal conditions for plant survival and is the result of a complex interaction between molecular processes, seed characteristics, and environmental cues. To detangle these processes, we made use of natural genetic variation present in an Arabidopsis (Arabidopsis thaliana) Bayreuth × Shahdara recombinant inbred line population. For a detailed analysis of the germination response, we characterized rate, uniformity, and maximum germination and discuss the added value of such precise measurements. The effects of after-ripening, stratification, and controlled deterioration as well as the effects of salt, mannitol, heat, cold, and abscisic acid (ABA) with and without cold stratification were analyzed for these germination characteristics. Seed morphology (size and length) of both dry and imbibed seeds was quantified by using image analysis. For the overwhelming amount of data produced in this study, we developed new approaches to perform and visualize high-throughput quantitative trait locus (QTL) analysis. We show correlation of trait data, (shared) QTL positions, and epistatic interactions. The detection of similar loci for different stresses indicates that, often, the molecular processes regulating environmental responses converge into similar pathways. Seven major QTL hotspots were confirmed using a heterogeneous inbred family approach. QTLs colocating with previously reported QTLs and well-characterized mutants are discussed. A new connection between dormancy, ABA, and a cripple mucilage formation due to a naturally occurring mutation in the MUCILAGE-MODIFIED2 gene is proposed, and this is an interesting lead for further research on the regulatory role of ABA in mucilage production and its multiple effects on germination parameters.
Collapse
|
18
|
Fu J, Wolfs MGM, Deelen P, Westra HJ, Fehrmann RSN, te Meerman GJ, Buurman WA, Rensen SSM, Groen HJM, Weersma RK, van den Berg LH, Veldink J, Ophoff RA, Snieder H, van Heel D, Jansen RC, Hofker MH, Wijmenga C, Franke L. Unraveling the regulatory mechanisms underlying tissue-dependent genetic variation of gene expression. PLoS Genet 2012; 8:e1002431. [PMID: 22275870 PMCID: PMC3261927 DOI: 10.1371/journal.pgen.1002431] [Citation(s) in RCA: 164] [Impact Index Per Article: 13.7] [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: 07/19/2011] [Accepted: 11/08/2011] [Indexed: 01/17/2023] Open
Abstract
It is known that genetic variants can affect gene expression, but it is not yet completely clear through what mechanisms genetic variation mediate this expression. We therefore compared the cis-effect of single nucleotide polymorphisms (SNPs) on gene expression between blood samples from 1,240 human subjects and four primary non-blood tissues (liver, subcutaneous, and visceral adipose tissue and skeletal muscle) from 85 subjects. We characterized four different mechanisms for 2,072 probes that show tissue-dependent genetic regulation between blood and non-blood tissues: on average 33.2% only showed cis-regulation in non-blood tissues; 14.5% of the eQTL probes were regulated by different, independent SNPs depending on the tissue of investigation. 47.9% showed a different effect size although they were regulated by the same SNPs. Surprisingly, we observed that 4.4% were regulated by the same SNP but with opposite allelic direction. We show here that SNPs that are located in transcriptional regulatory elements are enriched for tissue-dependent regulation, including SNPs at 3' and 5' untranslated regions (P = 1.84×10(-5) and 4.7×10(-4), respectively) and SNPs that are synonymous-coding (P = 9.9×10(-4)). SNPs that are associated with complex traits more often exert a tissue-dependent effect on gene expression (P = 2.6×10(-10)). Our study yields new insights into the genetic basis of tissue-dependent expression and suggests that complex trait associated genetic variants have even more complex regulatory effects than previously anticipated.
Collapse
Affiliation(s)
- Jingyuan Fu
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- * E-mail: (JF); (LF)
| | - Marcel G. M. Wolfs
- Department of Pathology and Medical Biology, Molecular Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Harm-Jan Westra
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Rudolf S. N. Fehrmann
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Gerard J. te Meerman
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Wim A. Buurman
- Department of Surgery, University Hospital Maastricht and Nutrition and Toxicology Research Institute (NUTRIM), Maastricht University, Maastricht, The Netherlands
| | - Sander S. M. Rensen
- Department of Surgery, University Hospital Maastricht and Nutrition and Toxicology Research Institute (NUTRIM), Maastricht University, Maastricht, The Netherlands
| | - Harry J. M. Groen
- Department of Pulmonology, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Rinse K. Weersma
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Leonard H. van den Berg
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jan Veldink
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Roel A. Ophoff
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Harold Snieder
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - David van Heel
- Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Ritsert C. Jansen
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
| | - Marten H. Hofker
- Department of Pathology and Medical Biology, Molecular Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- * E-mail: (JF); (LF)
| |
Collapse
|
19
|
Abstract
Genetical genomics combines acquired high-throughput genomic data with genetic analysis. In this chapter, we discuss the application of genetical genomics for evolutionary studies, where new high-throughput molecular technologies are combined with mapping quantitative trait loci (QTL) on the genome in segregating populations.The recent explosion of high-throughput data--measuring thousands of proteins and metabolites, deep sequencing, chromatin, and methyl-DNA immunoprecipitation--allows the study of the genetic variation underlying quantitative phenotypes, together termed xQTL. At the same time, mining information is not getting easier. To deal with the sheer amount of information, powerful statistical tools are needed to analyze multidimensional relationships. In the context of evolutionary computational biology, a well-designed experiment may help dissect a complex evolutionary trait using proven statistical methods for associating phenotypical variation with genomic locations.Evolutionary expression QTL (eQTL) studies of the last years focus on gene expression adaptations, mapping the gene expression landscape, and, tentatively, eQTL networks. Here, we discuss the possibility of introducing an evolutionary prior, in the form of gene families displaying evidence of positive selection, and using that in the context of an eQTL experiment for elucidating host-pathogen protein-protein interactions. Through the example of an experimental design, we discuss the choice of xQTL platform, analysis methods, and scope of results. The resulting eQTL can be matched, resulting in putative interacting genes and their regulators. In addition, a prior may help distinguish QTL causality from reactivity, or independence of traits, by creating QTL networks.
Collapse
Affiliation(s)
- Pjotr Prins
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands.
| | | | | |
Collapse
|
20
|
Fehrmann RSN, Jansen RC, Veldink JH, Westra HJ, Arends D, Bonder MJ, Fu J, Deelen P, Groen HJM, Smolonska A, Weersma RK, Hofstra RMW, Buurman WA, Rensen S, Wolfs MGM, Platteel M, Zhernakova A, Elbers CC, Festen EM, Trynka G, Hofker MH, Saris CGJ, Ophoff RA, van den Berg LH, van Heel DA, Wijmenga C, te Meerman GJ, Franke L. Trans-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA. PLoS Genet 2011; 7:e1002197. [PMID: 21829388 PMCID: PMC3150446 DOI: 10.1371/journal.pgen.1002197] [Citation(s) in RCA: 268] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Accepted: 06/06/2011] [Indexed: 12/19/2022] Open
Abstract
For many complex traits, genetic variants have been found associated. However, it is still mostly unclear through which downstream mechanism these variants cause these phenotypes. Knowledge of these intermediate steps is crucial to understand pathogenesis, while also providing leads for potential pharmacological intervention. Here we relied upon natural human genetic variation to identify effects of these variants on trans-gene expression (expression quantitative trait locus mapping, eQTL) in whole peripheral blood from 1,469 unrelated individuals. We looked at 1,167 published trait- or disease-associated SNPs and observed trans-eQTL effects on 113 different genes, of which we replicated 46 in monocytes of 1,490 different individuals and 18 in a smaller dataset that comprised subcutaneous adipose, visceral adipose, liver tissue, and muscle tissue. HLA single-nucleotide polymorphisms (SNPs) were 10-fold enriched for trans-eQTLs: 48% of the trans-acting SNPs map within the HLA, including ulcerative colitis susceptibility variants that affect plausible candidate genes AOAH and TRBV18 in trans. We identified 18 pairs of unlinked SNPs associated with the same phenotype and affecting expression of the same trans-gene (21 times more than expected, P<10−16). This was particularly pronounced for mean platelet volume (MPV): Two independent SNPs significantly affect the well-known blood coagulation genes GP9 and F13A1 but also C19orf33, SAMD14, VCL, and GNG11. Several of these SNPs have a substantially higher effect on the downstream trans-genes than on the eventual phenotypes, supporting the concept that the effects of these SNPs on expression seems to be much less multifactorial. Therefore, these trans-eQTLs could well represent some of the intermediate genes that connect genetic variants with their eventual complex phenotypic outcomes. Many genetic variants have been found associated with diseases. However, for many of these genetic variants, it remains unclear how they exert their effect on the eventual phenotype. We investigated genetic variants that are known to be associated with diseases and complex phenotypes and assessed whether these variants were also associated with gene expression levels in a set of 1,469 unrelated whole blood samples. For several diseases, such as type 1 diabetes and ulcerative colitis, we observed that genetic variants affect the expression of genes, not implicated before. For complex traits, such as mean platelet volume and mean corpuscular volume, we observed that independent genetic variants on different chromosomes influence the expression of exactly the same genes. For mean platelet volume, these genes include well-known blood coagulation genes but also genes with still unknown functions. These results indicate that, by systematically correlating genetic variation with gene expression levels, it is possible to identify downstream genes, which provide important avenues for further research.
Collapse
Affiliation(s)
- Rudolf S. N. Fehrmann
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Ritsert C. Jansen
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
| | - Jan H. Veldink
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Harm-Jan Westra
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Danny Arends
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
| | - Marc Jan Bonder
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Jingyuan Fu
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Patrick Deelen
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Harry J. M. Groen
- Department of Pulmonology, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Asia Smolonska
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Rinse K. Weersma
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
- Department of Gastroenterology and Hepatology, University Medical Centre Groningen and University of Groningen, Groningen, The Netherlands
| | - Robert M. W. Hofstra
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Wim A. Buurman
- NUTRIM School for Nutrition, Toxicology, and Metabolism, Department of General Surgery, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Sander Rensen
- NUTRIM School for Nutrition, Toxicology, and Metabolism, Department of General Surgery, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Marcel G. M. Wolfs
- Department of Pathology and Medical Biology, Medical Biology Section, Molecular Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Mathieu Platteel
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Alexandra Zhernakova
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Clara C. Elbers
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Eleanora M. Festen
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Gosia Trynka
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Marten H. Hofker
- Department of Pathology and Medical Biology, Medical Biology Section, Molecular Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Christiaan G. J. Saris
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Roel A. Ophoff
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Centre Utrecht, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
- Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Leonard H. van den Berg
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - David A. van Heel
- Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Gerard J. te Meerman
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
- Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- * E-mail:
| |
Collapse
|
21
|
Durrant C, Swertz MA, Alberts R, Arends D, Möller S, Mott R, Prins P, van der Velde KJ, Jansen RC, Schughart K. Bioinformatics tools and database resources for systems genetics analysis in mice--a short review and an evaluation of future needs. Brief Bioinform 2011; 13:135-42. [PMID: 22396485 PMCID: PMC3294237 DOI: 10.1093/bib/bbr026] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [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: 12/31/2022] Open
Abstract
During a meeting of the SYSGENET working group ‘Bioinformatics’, currently available software tools and databases for systems genetics in mice were reviewed and the needs for future developments discussed. The group evaluated interoperability and performed initial feasibility studies. To aid future compatibility of software and exchange of already developed software modules, a strong recommendation was made by the group to integrate HAPPY and R/qtl analysis toolboxes, GeneNetwork and XGAP database platforms, and TIQS and xQTL processing platforms. R should be used as the principal computer language for QTL data analysis in all platforms and a ‘cloud’ should be used for software dissemination to the community. Furthermore, the working group recommended that all data models and software source code should be made visible in public repositories to allow a coordinated effort on the use of common data structures and file formats.
Collapse
|
22
|
Westra HJ, Jansen RC, Fehrmann RSN, te Meerman GJ, van Heel D, Wijmenga C, Franke L. MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects. ACTA ACUST UNITED AC 2011; 27:2104-11. [PMID: 21653519 DOI: 10.1093/bioinformatics/btr323] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION Sample mix-ups can arise during sample collection, handling, genotyping or data management. It is unclear how often sample mix-ups occur in genome-wide studies, as there currently are no post hoc methods that can identify these mix-ups in unrelated samples. We have therefore developed an algorithm (MixupMapper) that can both detect and correct sample mix-ups in genome-wide studies that study gene expression levels. RESULTS We applied MixupMapper to five publicly available human genetical genomics datasets. On average, 3% of all analyzed samples had been assigned incorrect expression phenotypes: in one of the datasets 23% of the samples had incorrect expression phenotypes. The consequences of sample mix-ups are substantial: when we corrected these sample mix-ups, we identified on average 15% more significant cis-expression quantitative trait loci (cis-eQTLs). In one dataset, we identified three times as many significant cis-eQTLs after correction. Furthermore, we show through simulations that sample mix-ups can lead to an underestimation of the explained heritability of complex traits in genome-wide association datasets. AVAILABILITY AND IMPLEMENTATION MixupMapper is freely available at http://www.genenetwork.nl/mixupmapper/
Collapse
Affiliation(s)
- Harm-Jan Westra
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
23
|
Seinen E, Burgerhof JGM, Jansen RC, Sibon OCM. RNAi-induced off-target effects in Drosophila melanogaster: frequencies and solutions. Brief Funct Genomics 2011; 10:206-14. [PMID: 21596801 DOI: 10.1093/bfgp/elr017] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Genes can be silenced with short-interfering RNA molecules (siRNA). siRNAs are widely used to identify gene functions and have high potential for therapeutic treatments. It is critical that the siRNA specifically targets the expression of the gene of interest but has no off-target effects on other genes. Although siRNAs were initially considered to be exclusively active on mature mRNAs in the cytoplasm, additional studies have shown that siRNAs are present in the nucleus as well, suggesting that pre-mRNA sequences containing introns and other untranslated regions can also be targeted. In this study, we investigated the extent to which off-targets may occur in Drosophila melanogaster by looking at mature mRNA sequences and pre-mature RNA sequences separately. First, an in silico approach revealed that, based on sequence similarity, numerous off-targets are predicted to occur in RNAi experiments. Second, existing microarray data were used to investigate a possible effect of the predicted off-targets based on analysis of in vitro data. We found that the occurrence of off-targets in both mature and pre-mature RNA sequences in RNAi experiments can be extensive and significant. Possibilities are discussed how to minimize off-target effects.
Collapse
Affiliation(s)
- Erwin Seinen
- Section of Radiation & Stress Cell Biology, Department of Cell Biology, University Medical Center Groningen, The Netherlands
| | | | | | | |
Collapse
|
24
|
Scheltema RA, Jankevics A, Jansen RC, Swertz MA, Breitling R. PeakML/mzMatch: A File Format, Java Library, R Library, and Tool-Chain for Mass Spectrometry Data Analysis. Anal Chem 2011; 83:2786-93. [DOI: 10.1021/ac2000994] [Citation(s) in RCA: 239] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
25
|
|
26
|
Swertz MA, Dijkstra M, Adamusiak T, van der Velde JK, Kanterakis A, Roos ET, Lops J, Thorisson GA, Arends D, Byelas G, Muilu J, Brookes AJ, de Brock EO, Jansen RC, Parkinson H. The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button. BMC Bioinformatics 2010; 11 Suppl 12:S12. [PMID: 21210979 PMCID: PMC3040526 DOI: 10.1186/1471-2105-11-s12-s12] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [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: 11/10/2022] Open
Abstract
BACKGROUND There is a huge demand on bioinformaticians to provide their biologists with user friendly and scalable software infrastructures to capture, exchange, and exploit the unprecedented amounts of new *omics data. We here present MOLGENIS, a generic, open source, software toolkit to quickly produce the bespoke MOLecular GENetics Information Systems needed. METHODS The MOLGENIS toolkit provides bioinformaticians with a simple language to model biological data structures and user interfaces. At the push of a button, MOLGENIS' generator suite automatically translates these models into a feature-rich, ready-to-use web application including database, user interfaces, exchange formats, and scriptable interfaces. Each generator is a template of SQL, JAVA, R, or HTML code that would require much effort to write by hand. This 'model-driven' method ensures reuse of best practices and improves quality because the modeling language and generators are shared between all MOLGENIS applications, so that errors are found quickly and improvements are shared easily by a re-generation. A plug-in mechanism ensures that both the generator suite and generated product can be customized just as much as hand-written software. RESULTS In recent years we have successfully evaluated the MOLGENIS toolkit for the rapid prototyping of many types of biomedical applications, including next-generation sequencing, GWAS, QTL, proteomics and biobanking. Writing 500 lines of model XML typically replaces 15,000 lines of hand-written programming code, which allows for quick adaptation if the information system is not yet to the biologist's satisfaction. Each application generated with MOLGENIS comes with an optimized database back-end, user interfaces for biologists to manage and exploit their data, programming interfaces for bioinformaticians to script analysis tools in R, Java, SOAP, REST/JSON and RDF, a tab-delimited file format to ease upload and exchange of data, and detailed technical documentation. Existing databases can be quickly enhanced with MOLGENIS generated interfaces using the 'ExtractModel' procedure. CONCLUSIONS The MOLGENIS toolkit provides bioinformaticians with a simple model to quickly generate flexible web platforms for all possible genomic, molecular and phenotypic experiments with a richness of interfaces not provided by other tools. All the software and manuals are available free as LGPLv3 open source at http://www.molgenis.org.
Collapse
Affiliation(s)
- Morris A Swertz
- Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Department of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen, The Netherlands.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Abstract
MOTIVATION R/qtl is free and powerful software for mapping and exploring quantitative trait loci (QTL). R/qtl provides a fully comprehensive range of methods for a wide range of experimental cross types. We recently added multiple QTL mapping (MQM) to R/qtl. MQM adds higher statistical power to detect and disentangle the effects of multiple linked and unlinked QTL compared with many other methods. MQM for R/qtl adds many new features including improved handling of missing data, analysis of 10,000 s of molecular traits, permutation for determining significance thresholds for QTL and QTL hot spots, and visualizations for cis-trans and QTL interaction effects. MQM for R/qtl is the first free and open source implementation of MQM that is multi-platform, scalable and suitable for automated procedures and large genetical genomics datasets. AVAILABILITY R/qtl is free and open source multi-platform software for the statistical language R, and is made available under the GPLv3 license. R/qtl can be installed from http://www.rqtl.org/. R/qtl queries should be directed at the mailing list, see http://www.rqtl.org/list/. CONTACT kbroman@biostat.wisc.edu.
Collapse
Affiliation(s)
- Danny Arends
- Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands
| | | | | | | |
Collapse
|
28
|
Li Y, Tesson BM, Churchill GA, Jansen RC. Critical reasoning on causal inference in genome-wide linkage and association studies. Trends Genet 2010; 26:493-8. [PMID: 20951462 DOI: 10.1016/j.tig.2010.09.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 09/14/2010] [Accepted: 09/14/2010] [Indexed: 11/25/2022]
Abstract
Genome-wide linkage and association studies of tens of thousands of clinical and molecular traits are currently underway, offering rich data for inferring causality between traits and genetic variation. However, the inference process is based on discovering subtle patterns in the correlation between traits and is therefore challenging and could create a flood of untrustworthy causal inferences. Here we introduce the concerns and show that they are already valid in simple scenarios of two traits linked to or associated with the same genomic region. We argue that more comprehensive analysis and Bayesian reasoning are needed and that these can overcome some of the pitfalls, although not in every conceivable case. We conclude that causal inference methods can still be of use in the iterative process of mathematical modeling and biological validation.
Collapse
Affiliation(s)
- Yang Li
- Groningen Bioinformatics Centre, University of Groningen, The Netherlands
| | | | | | | |
Collapse
|
29
|
Tesson BM, Breitling R, Jansen RC. DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules. BMC Bioinformatics 2010; 11:497. [PMID: 20925918 PMCID: PMC2976757 DOI: 10.1186/1471-2105-11-497] [Citation(s) in RCA: 149] [Impact Index Per Article: 10.6] [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: 06/02/2010] [Accepted: 10/06/2010] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Large microarray datasets have enabled gene regulation to be studied through coexpression analysis. While numerous methods have been developed for identifying differentially expressed genes between two conditions, the field of differential coexpression analysis is still relatively new. More specifically, there is so far no sensitive and untargeted method to identify gene modules (also known as gene sets or clusters) that are differentially coexpressed between two conditions. Here, sensitive and untargeted means that the method should be able to construct de novo modules by grouping genes based on shared, but subtle, differential correlation patterns. RESULTS We present DiffCoEx, a novel method for identifying correlation pattern changes, which builds on the commonly used Weighted Gene Coexpression Network Analysis (WGCNA) framework for coexpression analysis. We demonstrate its usefulness by identifying biologically relevant, differentially coexpressed modules in a rat cancer dataset. CONCLUSIONS DiffCoEx is a simple and sensitive method to identify gene coexpression differences between multiple conditions.
Collapse
Affiliation(s)
- Bruno M Tesson
- Groningen Bioinformatics Center, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
| | | | | |
Collapse
|
30
|
Seinen E, Burgerhof JGM, Jansen RC, Sibon OCM. RNAi experiments in D. melanogaster: solutions to the overlooked problem of off-targets shared by independent dsRNAs. PLoS One 2010; 5. [PMID: 20957038 PMCID: PMC2948504 DOI: 10.1371/journal.pone.0013119] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Accepted: 09/01/2010] [Indexed: 11/19/2022] Open
Abstract
Background RNAi technology is widely used to downregulate specific gene products. Investigating the phenotype induced by downregulation of gene products provides essential information about the function of the specific gene of interest. When RNAi is applied in Drosophila melanogaster or Caenorhabditis elegans, often large dsRNAs are used. One of the drawbacks of RNAi technology is that unwanted gene products with sequence similarity to the gene of interest can be down regulated too. To verify the outcome of an RNAi experiment and to avoid these unwanted off-target effects, an additional non-overlapping dsRNA can be used to down-regulate the same gene. However it has never been tested whether this approach is sufficient to reduce the risk of off-targets. Methodology We created a novel tool to analyse the occurance of off-target effects in Drosophila and we analyzed 99 randomly chosen genes. Principal Findings Here we show that nearly all genes contain non-overlapping internal sequences that do show overlap in a common off-target gene. Conclusion Based on our in silico findings, off-target effects should not be ignored and our presented on-line tool enables the identification of two RNA interference constructs, free of overlapping off-targets, from any gene of interest.
Collapse
Affiliation(s)
- Erwin Seinen
- Section of Radiation and Stress Cell Biology, Department of Cell Biology, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Johannes G. M. Burgerhof
- Epidemiology, Faculty of Medical Sciences, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Ritsert C. Jansen
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
| | - Ody C. M. Sibon
- Section of Radiation and Stress Cell Biology, Department of Cell Biology, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
- * E-mail:
| |
Collapse
|
31
|
Swertz MA, Velde KJVD, Tesson BM, Scheltema RA, Arends D, Vera G, Alberts R, Dijkstra M, Schofield P, Schughart K, Hancock JM, Smedley D, Wolstencroft K, Goble C, de Brock EO, Jones AR, Parkinson HE, Jansen RC. XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments. Genome Biol 2010; 11:R27. [PMID: 20214801 PMCID: PMC2864567 DOI: 10.1186/gb-2010-11-3-r27] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [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: 07/14/2009] [Revised: 12/17/2009] [Accepted: 03/09/2010] [Indexed: 11/10/2022] Open
Abstract
XGAP, a software platform for the integration and analysis of genotype and phenotype data. We present an extensible software model for the genotype and phenotype community, XGAP. Readers can download a standard XGAP (http://www.xgap.org) or auto-generate a custom version using MOLGENIS with programming interfaces to R-software and web-services or user interfaces for biologists. XGAP has simple load formats for any type of genotype, epigenotype, transcript, protein, metabolite or other phenotype data. Current functionality includes tools ranging from eQTL analysis in mouse to genome-wide association studies in humans.
Collapse
Affiliation(s)
- Morris A Swertz
- Genomics Coordination Center, Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Johannes F, Wardenaar R, Colomé-Tatché M, Mousson F, de Graaf P, Mokry M, Guryev V, Timmers HTM, Cuppen E, Jansen RC. Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq. ACTA ACUST UNITED AC 2010; 26:1000-6. [PMID: 20208068 DOI: 10.1093/bioinformatics/btq087] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION ChIP-chip and ChIP-seq technologies provide genome-wide measurements of various types of chromatin marks at an unprecedented resolution. With ChIP samples collected from different tissue types and/or individuals, we can now begin to characterize stochastic or systematic changes in epigenetic patterns during development (intra-individual) or at the population level (inter-individual). This requires statistical methods that permit a simultaneous comparison of multiple ChIP samples on a global as well as locus-specific scale. Current analytical approaches are mainly geared toward single sample investigations, and therefore have limited applicability in this comparative setting. This shortcoming presents a bottleneck in biological interpretations of multiple sample data. RESULTS To address this limitation, we introduce a parametric classification approach for the simultaneous analysis of two (or more) ChIP samples. We consider several competing models that reflect alternative biological assumptions about the global distribution of the data. Inferences about locus-specific and genome-wide chromatin differences are reached through the estimation of multivariate mixtures. Parameter estimates are obtained using an incremental version of the Expectation-Maximization algorithm (IEM). We demonstrate efficient scalability and application to three very diverse ChIP-chip and ChIP-seq experiments. The proposed approach is evaluated against several published ChIP-chip and ChIP-seq software packages. We recommend its use as a first-pass algorithm to identify candidate regions in the epigenome, possibly followed by some type of second-pass algorithm to fine-tune detected peaks in accordance with biological or technological criteria. AVAILABILITY R source code is available at http://gbic.biol.rug.nl/supplementary/2009/ChromatinProfiles/. Access to Chip-seq data: GEO repository GSE17937.
Collapse
Affiliation(s)
- Frank Johannes
- Groningen Bioinformatics Centre, University of Groningen, Kerklaan 30, Biologisch Centrum, 9751 NN Haren, The Netherlands.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
|
34
|
Li Y, Swertz MA, Vera G, Fu J, Breitling R, Jansen RC. designGG: an R-package and web tool for the optimal design of genetical genomics experiments. BMC Bioinformatics 2009; 10:188. [PMID: 19538731 PMCID: PMC2706229 DOI: 10.1186/1471-2105-10-188] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Accepted: 06/18/2009] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND High-dimensional biomolecular profiling of genetically different individuals in one or more environmental conditions is an increasingly popular strategy for exploring the functioning of complex biological systems. The optimal design of such genetical genomics experiments in a cost-efficient and effective way is not trivial. RESULTS This paper presents designGG, an R package for designing optimal genetical genomics experiments. A web implementation for designGG is available at http://gbic.biol.rug.nl/designGG. All software, including source code and documentation, is freely available. CONCLUSION DesignGG allows users to intelligently select and allocate individuals to experimental units and conditions such as drug treatment. The user can maximize the power and resolution of detecting genetic, environmental and interaction effects in a genome-wide or local mode by giving more weight to genome regions of special interest, such as previously detected phenotypic quantitative trait loci. This will help to achieve high power and more accurate estimates of the effects of interesting factors, and thus yield a more reliable biological interpretation of data. DesignGG is applicable to linkage analysis of experimental crosses, e.g. recombinant inbred lines, as well as to association analysis of natural populations.
Collapse
Affiliation(s)
- Yang Li
- Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
| | - Morris A Swertz
- Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Gonzalo Vera
- Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
| | - Jingyuan Fu
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Rainer Breitling
- Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
| | - Ritsert C Jansen
- Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| |
Collapse
|
35
|
Jansen RC, Tesson BM, Fu J, Yang Y, McIntyre LM. Defining gene and QTL networks. Curr Opin Plant Biol 2009; 12:241-246. [PMID: 19196544 DOI: 10.1016/j.pbi.2009.01.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Revised: 01/06/2009] [Accepted: 01/06/2009] [Indexed: 05/27/2023]
Abstract
Current technologies for high-throughput molecular profiling of large numbers of genetically different individuals offer great potential for elucidating the genotype-to-phenotype relationship. Variation in molecular and phenotypic traits can be correlated to DNA sequence variation using the methods of quantitative trait locus (QTL) mapping. In addition, the correlation structure in the molecular and phenotypic traits can be informative for inferring the underlying molecular networks. For this, new methods are emerging to distinguish among causality, reactivity, or independence of traits based upon logic involving underlying QTL. These methods are becoming increasingly popular in plant genetic studies as well as in studies on many other organisms.
Collapse
Affiliation(s)
- Ritsert C Jansen
- Groningen Bioinformatics Centre, University of Groningen, The Netherlands
| | | | | | | | | |
Collapse
|
36
|
Heap GA, Trynka G, Jansen RC, Bruinenberg M, Swertz MA, Dinesen LC, Hunt KA, Wijmenga C, Vanheel DA, Franke L. Complex nature of SNP genotype effects on gene expression in primary human leucocytes. BMC Med Genomics 2009; 2:1. [PMID: 19128478 PMCID: PMC2628677 DOI: 10.1186/1755-8794-2-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [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: 06/03/2008] [Accepted: 01/07/2009] [Indexed: 12/12/2022] Open
Abstract
Background Genome wide association studies have been hugely successful in identifying disease risk variants, yet most variants do not lead to coding changes and how variants influence biological function is usually unknown. Methods We correlated gene expression and genetic variation in untouched primary leucocytes (n = 110) from individuals with celiac disease – a common condition with multiple risk variants identified. We compared our observations with an EBV-transformed HapMap B cell line dataset (n = 90), and performed a meta-analysis to increase power to detect non-tissue specific effects. Results In celiac peripheral blood, 2,315 SNP variants influenced gene expression at 765 different transcripts (< 250 kb from SNP, at FDR = 0.05, cis expression quantitative trait loci, eQTLs). 135 of the detected SNP-probe effects (reflecting 51 unique probes) were also detected in a HapMap B cell line published dataset, all with effects in the same allelic direction. Overall gene expression differences within the two datasets predominantly explain the limited overlap in observed cis-eQTLs. Celiac associated risk variants from two regions, containing genes IL18RAP and CCR3, showed significant cis genotype-expression correlations in the peripheral blood but not in the B cell line datasets. We identified 14 genes where a SNP affected the expression of different probes within the same gene, but in opposite allelic directions. By incorporating genetic variation in co-expression analyses, functional relationships between genes can be more significantly detected. Conclusion In conclusion, the complex nature of genotypic effects in human populations makes the use of a relevant tissue, large datasets, and analysis of different exons essential to enable the identification of the function for many genetic risk variants in common diseases.
Collapse
Affiliation(s)
- Graham A Heap
- Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, London, E1 2AT, UK.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Scheltema RA, Kamleh A, Wildridge D, Ebikeme C, Watson DG, Barrett MP, Jansen RC, Breitling R. Increasing the mass accuracy of high-resolution LC-MS data using background ions - a case study on the LTQ-Orbitrap. Proteomics 2008; 8:4647-56. [DOI: 10.1002/pmic.200800314] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
38
|
Breitling R, Li Y, Tesson BM, Fu J, Wu C, Wiltshire T, Gerrits A, Bystrykh LV, de Haan G, Su AI, Jansen RC. Genetical genomics: spotlight on QTL hotspots. PLoS Genet 2008; 4:e1000232. [PMID: 18949031 PMCID: PMC2563687 DOI: 10.1371/journal.pgen.1000232] [Citation(s) in RCA: 164] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Rainer Breitling
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, Haren, The Netherlands
| | - Yang Li
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, Haren, The Netherlands
| | - Bruno M. Tesson
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, Haren, The Netherlands
| | - Jingyuan Fu
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, Haren, The Netherlands
- Department of Human Genetics, Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Chunlei Wu
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Tim Wiltshire
- School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Alice Gerrits
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Leonid V. Bystrykh
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Gerald de Haan
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Andrew I. Su
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
- * E-mail: (AIS); (RCJ)
| | - Ritsert C. Jansen
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, Haren, The Netherlands
- Department of Human Genetics, Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- * E-mail: (AIS); (RCJ)
| |
Collapse
|
39
|
Abstract
BACKGROUND R is the preferred tool for statistical analysis of many bioinformaticians due in part to the increasing number of freely available analytical methods. Such methods can be quickly reused and adapted to each particular experiment. However, in experiments where large amounts of data are generated, for example using high-throughput screening devices, the processing time required to analyze data is often quite long. A solution to reduce the processing time is the use of parallel computing technologies. Because R does not support parallel computations, several tools have been developed to enable such technologies. However, these tools require multiple modications to the way R programs are usually written or run. Although these tools can finally speed up the calculations, the time, skills and additional resources required to use them are an obstacle for most bioinformaticians. RESULTS We have designed and implemented an R add-on package, R/parallel, that extends R by adding user-friendly parallel computing capabilities. With R/parallel any bioinformatician can now easily automate the parallel execution of loops and benefit from the multicore processor power of today's desktop computers. Using a single and simple function, R/parallel can be integrated directly with other existing R packages. With no need to change the implemented algorithms, the processing time can be approximately reduced N-fold, N being the number of available processor cores. CONCLUSION R/parallel saves bioinformaticians time in their daily tasks of analyzing experimental data. It achieves this objective on two fronts: first, by reducing development time of parallel programs by avoiding reimplementation of existing methods and second, by reducing processing time by speeding up computations on current desktop computers. Future work is focused on extending the envelope of R/parallel by interconnecting and aggregating the power of several computers, both existing office computers and computing clusters.
Collapse
Affiliation(s)
- Gonzalo Vera
- Computer Architecture and Operating Systems Department, Universitat Autònoma de Barcelona, Bellaterra, Spain.
| | | | | |
Collapse
|
40
|
Li Y, Breitling R, Jansen RC. Generalizing genetical genomics: getting added value from environmental perturbation. Trends Genet 2008; 24:518-24. [PMID: 18774198 DOI: 10.1016/j.tig.2008.08.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2007] [Revised: 08/08/2008] [Accepted: 08/09/2008] [Indexed: 11/29/2022]
Abstract
Genetical genomics is a useful approach for studying the effect of genetic perturbations on biological systems at the molecular level. However, molecular networks depend on the environmental conditions and, thus, a comprehensive understanding of biological systems requires studying them across multiple environments. We propose a generalization of genetical genomics, which combines genetic and sensibly chosen environmental perturbations, to study the plasticity of molecular networks. This strategy forms a crucial step toward understanding why individuals respond differently to drugs, toxins, pathogens, nutrients and other environmental influences. Here we outline a strategy for selecting and allocating individuals to particular treatments, and we discuss the promises and pitfalls of the generalized genetical genomics approach.
Collapse
Affiliation(s)
- Yang Li
- Groningen Bioinformatics Centre, University of Groningen, 9751 NN Haren, The Netherlands
| | | | | |
Collapse
|
41
|
Nolte IM, de Vries AR, Spijker GT, Jansen RC, Brinza D, Zelikovsky A, Te Meerman GJ. Association testing by haplotype-sharing methods applicable to whole-genome analysis. BMC Proc 2007; 1 Suppl 1:S129. [PMID: 18466471 PMCID: PMC2367507 DOI: 10.1186/1753-6561-1-s1-s129] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [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: 01/09/2023] Open
Abstract
We propose two new haplotype-sharing methods for identifying disease loci: the haplotype sharing statistic (HSS), which compares length of shared haplotypes between cases and controls, and the CROSS test, which tests whether a case and a control haplotype show less sharing than two random haplotypes. The significance of the HSS is determined using a variance estimate from the theory of U-statistics, whereas the significance of the CROSS test is estimated from a sequential randomization procedure. Both methods are fast and hence practical, even for whole-genome screens with high marker densities. We analyzed data sets of Problems 2 and 3 of Genetic Analysis Workshop 15 and compared HSS and CROSS to conventional association methods. Problem 2 provided a data set of 2300 single-nucleotide polymorphisms (SNPs) in a 10-Mb region of chromosome 18q, which had shown linkage evidence for rheumatoid arthritis. The CROSS test detected a significant association at approximately position 4407 kb. This was supported by single-marker association and HSS. The CROSS test outperformed them both with respect to significance level and signal-to-noise ratio. A 20-kb candidate region could be identified. Problem 3 provided a simulated 10 k SNP data set covering the whole genome. Three known candidate regions for rheumatoid arthritis were detected. Again, the CROSS test gave the most significant results. Furthermore, both the HSS and the CROSS showed better fine-mapping accuracy than straightforward haplotype association. In conclusion, haplotype sharing methods, particularly the CROSS test, show great promise for identifying disease gene loci.
Collapse
Affiliation(s)
- Ilja M Nolte
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, the Netherlands
| | - André R de Vries
- Department of Genetics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, the Netherlands
| | - Geert T Spijker
- Deparment of Dermatology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, the Netherlands
| | - Ritsert C Jansen
- Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, the Netherlands
| | - Dumitru Brinza
- Department of Computer Science, Georgia State University, 34 Peachtree Street, Atlanta, Georgia 30303-3086, USA
| | - Alexander Zelikovsky
- Department of Computer Science, Georgia State University, 34 Peachtree Street, Atlanta, Georgia 30303-3086, USA
| | - Gerard J Te Meerman
- Department of Genetics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, the Netherlands
| |
Collapse
|
42
|
Abstract
MOTIVATION Affymetrix arrays use multiple probes per gene to measure mRNA abundances. Standard software takes averages over probes. Important information may be lost if polymorphisms in the mRNA affect the hybridization of individual probes. RESULTS We present custom software to analyze genetical genomics experiments in human, mouse and other organisms: (i) an R package providing functions for QTL analysis at the individual probe level and (ii) Perl scripts providing custom tracks in the UCSC Genome Browser to check for sequence polymorphisms in probe regions. AVAILABILITY http://gbic.biol.rug.nl/supplementary.
Collapse
Affiliation(s)
- Rudi Alberts
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
| | | | | |
Collapse
|
43
|
Nyangoma SO, van Kampen AAHC, Reijmers TH, Govorukhina NI, van der Zee AGJ, Billingham LJ, Bischoff R, Jansen RC. Multiple testing issues in discriminating compound-related peaks and chromatograms from high frequency noise, spikes and solvent-based noise in LC-MS data sets. Stat Appl Genet Mol Biol 2007; 6:Article23. [PMID: 17910529 DOI: 10.2202/1544-6115.1295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 11/18/2022]
Abstract
Liquid Chromatography--Mass Spectrometry (LC-MS) is a powerful method for sensitive detection and quantification of proteins and peptides in complex biological fluids like serum. LC-MS produces complex data sets, consisting of some hundreds of millions of data points per sample at a resolution of 0.1 amu in the m/z domain and 7000 data points in the time domain. However, the detection of the lower abundance proteins from this data is hampered by the presence of artefacts, such as high frequency noise and spikes. Moreover, not all of the tens of thousands of the chromatograms produced per sample are relevant for the pursuit of the biomarkers. Thus in analysing the LC-MS data, two critical pre-processing issues arise. Which of the thousands of the: 1. chromatograms per sample are relevant for the detection of the biomarkers?, and 2. signals per chromatogram are truly compound-related? Each of these issues involves assessing the significance (deviation from noise) of multiple observations and the issue of multiple comparisons arises. Current methods disregard the multiplicity and provide no concrete threshold for significance. However, with such procedures, the probability of one or more false-positives is high as the number of tests to be performed is large, and must be controlled. Realizing that the cut-offs for declaring a chromatogram (or a signal) to be compound-related can hugely influence which proteins are detected, it seems natural to define thresholds that are neither arbitrary nor subjective. We suggest the choice of thresholds guided by the critical aim of controlling the False Discovery Rate (FDR) in multiple hypotheses testing for significance over a large set of features produced per sample. This involves the use of the regression diagnostics to characterize the signals of a chromatogram (e.g. as outliers or influential) and to suggest suitable tests statistics for the multiple testing procedures (MTP) for discriminating noise and spikes from true signals. The role of the Generalized Linear Models (GLM) in this MTP is investigated. The method is applied to LC-MS datasets from trypsin-digested serum spiked with varying levels of horse heart cytochrome C (cytoc).
Collapse
|
44
|
Abstract
Many investigations have reported the successful mapping of quantitative trait loci (QTLs) for gene expression phenotypes (eQTLs). Local eQTLs, where expression phenotypes map to the genes themselves, are of especially great interest, because they are direct candidates for previously mapped physiological QTLs. Here we show that many mapped local eQTLs in genetical genomics experiments do not reflect actual expression differences caused by sequence polymorphisms in cis-acting factors changing mRNA levels. Instead they indicate hybridization differences caused by sequence polymorphisms in the mRNA region that is targeted by the microarray probes. Many such polymorphisms can be detected by a sensitive and novel statistical approach that takes the individual probe signals into account. Applying this approach to recent mouse and human eQTL data, we demonstrate that indeed many local eQTLs are falsely reported as “cis-acting” or “cis” and can be successfully detected and eliminated with this approach.
Collapse
Affiliation(s)
- Rudi Alberts
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
| | - Peter Terpstra
- Groningen Bioinformatics Centre, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Yang Li
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
| | - Rainer Breitling
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
| | - Jan-Peter Nap
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
- Bioinformatics Expertise Center, Institute for Life Science and Technology, Hanze University Groningen, University for Applied Sciences, Groningen, The Netherlands
| | - Ritsert C. Jansen
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
- Groningen Bioinformatics Centre, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|
45
|
Abstract
We here describe the MetaNetwork protocol to reconstruct metabolic networks using metabolite abundance data from segregating populations. MetaNetwork maps metabolite quantitative trait loci (mQTLs) underlying variation in metabolite abundance in individuals of a segregating population using a two-part model to account for the often observed spike in the distribution of metabolite abundance data. MetaNetwork predicts and visualizes potential associations between metabolites using correlations of mQTL profiles, rather than of abundance profiles. Simulation and permutation procedures are used to assess statistical significance. Analysis of about 20 metabolite mass peaks from a mass spectrometer takes a few minutes on a desktop computer. Analysis of 2,000 mass peaks will take up to 4 days. In addition, MetaNetwork is able to integrate high-throughput data from subsequent metabolomics, transcriptomics and proteomics experiments in conjunction with traditional phenotypic data. This way MetaNetwork will contribute to a better integration of such data into systems biology.
Collapse
Affiliation(s)
- Jingyuan Fu
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, NL-9751 NN Haren, The Netherlands
| | | | | | | |
Collapse
|
46
|
Alberts R, Terpstra P, Hardonk M, Bystrykh LV, de Haan G, Breitling R, Nap JP, Jansen RC. A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat. BMC Bioinformatics 2007; 8:132. [PMID: 17448222 PMCID: PMC1865557 DOI: 10.1186/1471-2105-8-132] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2006] [Accepted: 04/20/2007] [Indexed: 01/09/2023] Open
Abstract
Background The Affymetrix GeneChip technology uses multiple probes per gene to measure its expression level. Individual probe signals can vary widely, which hampers proper interpretation. This variation can be caused by probes that do not properly match their target gene or that match multiple genes. To determine the accuracy of Affymetrix arrays, we developed an extensive verification protocol, for mouse arrays incorporating the NCBI RefSeq, NCBI UniGene Unique, NIA Mouse Gene Index, and UCSC mouse genome databases. Results Applying this protocol to Affymetrix Mouse Genome arrays (the earlier U74Av2 and the newer 430 2.0 array), the number of sequence-verified probes with perfect matches was no less than 85% and 95%, respectively; and for 74% and 85% of the probe sets all probes were sequence verified. The latter percentages increased to 80% and 94% after discarding one or two unverifiable probes per probe set, and even further to 84% and 97% when, in addition, allowing for one or two mismatches between probe and target gene. Similar results were obtained for other mouse arrays, as well as for human and rat arrays. Based on these data, refined chip definition files for all arrays are provided online. Researchers can choose the version appropriate for their study to (re)analyze expression data. Conclusion The accuracy of Affymetrix probe sequences is higher than previously reported, particularly on newer arrays. Yet, refined probe set definitions have clear effects on the detection of differentially expressed genes. We demonstrate that the interpretation of the results of Affymetrix arrays is improved when the new chip definition files are used.
Collapse
Affiliation(s)
- Rudi Alberts
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751 NN Haren, The Netherlands
| | - Peter Terpstra
- Groningen Bioinformatics Centre, University Medical Centre Groningen, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Menno Hardonk
- Groningen Bioinformatics Centre, University Medical Centre Groningen, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Leonid V Bystrykh
- Department of Cell Biology, section Stem Cell Biology, University Medical Centre Groningen, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Gerald de Haan
- Department of Cell Biology, section Stem Cell Biology, University Medical Centre Groningen, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Rainer Breitling
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751 NN Haren, The Netherlands
| | - Jan-Peter Nap
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751 NN Haren, The Netherlands
- Bioinformatics Expertise Center, Institute for Life Science & Technology, Hanze University Groningen, 9747 AS Groningen, The Netherlands
| | - Ritsert C Jansen
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751 NN Haren, The Netherlands
- Groningen Bioinformatics Centre, University Medical Centre Groningen, University of Groningen, 9713 AV Groningen, The Netherlands
| |
Collapse
|
47
|
Abstract
Progress in systems biology is seriously hindered by slow production of suitable software infrastructures. Biologists need infrastructure that easily connects to work that is done in other laboratories, for which standardization is helpful. However, the infrastructure must also accommodate the specifics of their biological system, but appropriate mechanisms to support variation are currently lacking. We argue that a minimal computer language, and a software tool called a generator, can be used to quickly produce customized software infrastructures that 'systems biologists really want to have'.
Collapse
Affiliation(s)
- Morris A Swertz
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, NL-9751 NN Haren, The Netherlands
| | | |
Collapse
|
48
|
Dijkstra M, Vonk RJ, Jansen RC. SELDI-TOF mass spectra: A view on sources of variation. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 847:12-23. [PMID: 17118720 DOI: 10.1016/j.jchromb.2006.11.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2006] [Revised: 10/27/2006] [Accepted: 11/05/2006] [Indexed: 10/23/2022]
Abstract
Adequate interpretation of mass spectrometry data can yield valuable biomarkers. However, spectrum interpretation is a complicated task. This paper reviews the various factors that determine a sample's spectrum and demonstrates the role of these factors in the interpretation process. We derive a simulation model that adequately predicts the expected spectrum based on known sample content and, in the reverse mode, obtain an analysis model that adequately fits an observed spectrum based on the hypothesized sources of variation.
Collapse
Affiliation(s)
- Martijn Dijkstra
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, P.O. Box 800, NL-9700 AV Groningen, The Netherlands.
| | | | | |
Collapse
|
49
|
Keurentjes JJB, Fu J, Terpstra IR, Garcia JM, van den Ackerveken G, Snoek LB, Peeters AJM, Vreugdenhil D, Koornneef M, Jansen RC. Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci. Proc Natl Acad Sci U S A 2007; 104:1708-13. [PMID: 17237218 PMCID: PMC1785256 DOI: 10.1073/pnas.0610429104] [Citation(s) in RCA: 227] [Impact Index Per Article: 13.4] [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: 01/04/2023] Open
Abstract
Accessions of a plant species can show considerable genetic differences that are analyzed effectively by using recombinant inbred line (RIL) populations. Here we describe the results of genome-wide expression variation analysis in an RIL population of Arabidopsis thaliana. For many genes, variation in expression could be explained by expression quantitative trait loci (eQTLs). The nature and consequences of this variation are discussed based on additional genetic parameters, such as heritability and transgression and by examining the genomic position of eQTLs versus gene position, polymorphism frequency, and gene ontology. Furthermore, we developed an approach for genetic regulatory network construction by combining eQTL mapping and regulator candidate gene selection. The power of our method was shown in a case study of genes associated with flowering time, a well studied regulatory network in Arabidopsis. Results that revealed clusters of coregulated genes and their most likely regulators were in agreement with published data, and unknown relationships could be predicted.
Collapse
Affiliation(s)
- Joost J. B. Keurentjes
- Laboratories of *Genetics and
- Plant Physiology, Wageningen University, Arboretumlaan 4, NL-6703 BD Wageningen, The Netherlands
- To whom correspondence may be addressed. E-mail:
or
| | - Jingyuan Fu
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30 NL-9751 NN Haren, The Netherlands
| | - Inez R. Terpstra
- Molecular Genetics Group, Department of Biology, Utrecht University, Padualaan 8, NL-3584 CH Utrecht, The Netherlands
| | - Juan M. Garcia
- Molecular Genetics Group, Department of Biology, Utrecht University, Padualaan 8, NL-3584 CH Utrecht, The Netherlands
| | - Guido van den Ackerveken
- Molecular Genetics Group, Department of Biology, Utrecht University, Padualaan 8, NL-3584 CH Utrecht, The Netherlands
| | - L. Basten Snoek
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Sorbonnelaan 16, NL-3584 CA Utrecht, The Netherlands; and
| | - Anton J. M. Peeters
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Sorbonnelaan 16, NL-3584 CA Utrecht, The Netherlands; and
| | - Dick Vreugdenhil
- Plant Physiology, Wageningen University, Arboretumlaan 4, NL-6703 BD Wageningen, The Netherlands
| | - Maarten Koornneef
- Laboratories of *Genetics and
- **Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
- To whom correspondence may be addressed. E-mail:
or
| | - Ritsert C. Jansen
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30 NL-9751 NN Haren, The Netherlands
| |
Collapse
|
50
|
Abstract
Surface-enhanced laser desorption/ionization (SELDI) time of flight (TOF) is a mass spectrometry technology for measuring the composition of a sampled protein mixture. A mass spectrum contains peaks corresponding to proteins in the sample. The peak areas are proportional to the measured concentrations of the corresponding proteins. Quantifying peak areas is difficult for existing methods because peak shapes are not constant across a spectrum and because peaks often overlap. We present a new method for quantifying peak areas. Our method decomposes a spectrum into peaks and a baseline using so-called statistical finite mixture models. We illustrate our method in detail on 8 samples from culture media of adipose tissue and globally on 64 samples from serum to compare our method to the standard Ciphergen method. Both methods give similar estimates for singleton peaks, but not for overlapping peaks. The Ciphergen method overestimates the heights of such peaks while our method still gives appropriate estimates. Peak quantification is an important step in pre-processing SELDI-TOF data and improvements therein will pay off in the later biomarker discovery phase.
Collapse
Affiliation(s)
- Martijn Dijkstra
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
| | | | | | | |
Collapse
|