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Genomics Core Facility

Next generation sequencing, also sometimes called deep sequencing, is our core business. We have a team of over 10 people, both wet lab technicians and bioinformaticians, to support the research and the clinical application of this technology using multiple Illumina HiSeq2000 and MiSeq machines.

The applications for this technology are widespread, still growing and are common practice in the institute. Every aspect of the deep sequencing process is supported by the GCF that, as a facility, has a large body of experience and knowledge. The facility has been using Illumina technology from the early onset of the NGS development in 2009 and therefore we are now in a position to support the users with clear advice as to how the experiment should be designed to increase the success rate of the experiment.  We are open to suggestions and are flexible in the way users want to have their samples analyzed with regard to sequence depth and numbers of libraries that are pooled in multiplexed experiments.

The facility is set up according to a fee-for-service model where the material and chemistry cost prize is the main factor that determines the fee, this makes our support very affordable compared to external service providers. 

Facility users can provide cells or tissues as starting material but we also work with purified RNA or DNA as well as ready to sequence DNA libraries. All the necessary equipment for the preparation of sequence libraries and the associated quality control steps are in house. For some applications, like RNAseq, the demand is so high that we run the sample preparation in 96-wells format using PE SciClone robotic pipetting systems.

The bulk of the experiments are performed using validated Illumina protocols and kits, but extensive experience has made it possible to either adapt, or develop new protocols for creating sequencing libraries. This is often done in close collaboration with the end user. New developments are closely followed and can be implemented relatively quickly.

The data generated by the sequencing machines is stored on a central server system and analyzed by the facilities bioinformaticians. All data can also be made directly available to the user in the desired format. We have pipelines for demultiplexing the data, the alignment of the reads to genomes of choice and experiment specific downstream analysis. We can provide the results in tabular or graphical formats or prepare them for visualization in genome viewers like IGV (http://www.broad.mit.edu/igv/). We also host licenses for third party software solutions for analysis like Ingenuity and Nexus.

Equipment

HiSeq2000 (2x), MiSeq, cBot, Perkin Elmer NGSx Sciclone Workstation, Covaris, Agilent BioAnalyzer, Perkin Elmer-Gx system, Biomek Fx, Agilent Scanner, Illumina Beadarray Reader, Tecan Hybstations, Nimblegen Hybstation, MicroGrid Printrobot.

Published Manuscripts:

1.Drug-induced histone eviction from open chromatin contributes to the chemotherapeutic effects of doxorubicin.
Pang B, Qiao X, Janssen L, Velds A, Groothuis T, Kerkhoven R, Nieuwland M, Ovaa H, Rottenberg S, van Tellingen O, Janssen J, Huijgens P, Zwart W, Neefjes J. Nat Commun. 2013 May 28;4:1908. doi: 10.1038/ncomms2921. PMID: 23715267 [PubMed - in process]

2.Identification of recurrent FGFR3 fusion genes in lung cancer through kinome-centered RNA sequencing.
Majewski IJ, Mittempergher L, Davidson NM, Bosma A, Willems SM, Horlings HM, de Rink I, Greger L, Hooijer GK, Peters D, Nederlof PM, Hofland I, de Jong J, Wesseling J, Kluin RJ, Brugman W, Kerkhoven R, Nieboer F, Roepman P, Broeks A, Muley TR, Jassem J, Niklinski J, van Zandwijk N, Brazma A, Oshlack A, van den Heuvel M, Bernards R.
J Pathol. 2013 May 9. doi: 10.1002/path.4209. [Epub ahead of print]
PMID: 23661334 [PubMed - as supplied by publisher]

3.Deciphering the glycosylome of dystroglycanopathies using haploid screens for lassa virus entry.
Jae LT, Raaben M, Riemersma M, van Beusekom E, Blomen VA, Velds A, Kerkhoven RM, Carette JE, Topaloglu H, Meinecke P, Wessels MW, Lefeber DJ, Whelan SP, van Bokhoven H, Brummelkamp TR.Science. 2013 Apr 26;340(6131):479-83. doi: 10.1126/science.1233675. Epub 2013 Mar 21.PMID: 23519211 [PubMed - indexed for MEDLINE]

4.Dosage-dependent tumor suppression by histone deacetylases 1 and 2 through regulation of c-Myc collaborating genes and p53 function.
Heideman MR, Wilting RH, Yanover E, Velds A, de Jong J, Kerkhoven RM, Jacobs H, Wessels LF, Dannenberg JH.Blood. 2013 Mar 14;121(11):2038-50. doi: 10.1182/blood-2012-08-450916. Epub 2013 Jan 17.PMID: 23327920 [PubMed - indexed for MEDLINE] Free PMC Article

5.SERPINA6, BEX1, AGTR1, SLC26A3, and LAPTM4B are markers of resistance to neoadjuvant chemotherapy in HER2-negative breast cancer.
de Ronde JJ, Lips EH, Mulder L, Vincent AD, Wesseling J, Nieuwland M, Kerkhoven R, Vrancken Peeters MJ, Sonke GS, Rodenhuis S, Wessels LF.Breast Cancer Res Treat. 2013 Jan;137(1):213-23. doi: 10.1007/s10549-012-2340-x. Epub 2012 Dec 1.PMID: 23203637 [PubMed - indexed for MEDLINE]

6.Glucosylated hydroxymethyluracil, DNA base J, prevents transcriptional readthrough in Leishmania.
van Luenen HG, Farris C, Jan S, Genest PA, Tripathi P, Velds A, Kerkhoven RM, Nieuwland M, Haydock A, Ramasamy G, Vainio S, Heidebrecht T, Perrakis A, Pagie L, van Steensel B, Myler PJ, Borst P.Cell. 2012 Aug 31;150(5):909-21. doi: 10.1016/j.cell.2012.07.030.PMID: 22939620 [PubMed - indexed for MEDLINE]
 
7.Reassessing genomic targeting of AID.
Hogenbirk MA, Velds A, Kerkhoven RM, Jacobs H.Nat Immunol. 2012 Sep;13(9):797-8; author reply 798-800. doi: 10.1038/ni.2367. No abstract available. PMID: 22910380 [PubMed - indexed for MEDLINE]

8.Search for a gene expression signature of breast cancer local recurrence in young women.
Servant N, Bollet MA, Halfwerk H, Bleakley K, Kreike B, Jacob L, Sie D, Kerkhoven RM, Hupé P, Hadhri R, Fourquet A, Bartelink H, Barillot E, Sigal-Zafrani B, van de Vijver MJ.Clin Cancer Res. 2012 Mar 15;18(6):1704-15. doi: 10.1158/1078-0432.CCR-11-1954. Epub 2012 Jan 23.PMID: 22271875 [PubMed - indexed for MEDLINE] Free Article
 
9.A barcode screen for epigenetic regulators reveals a role for the NuB4/HAT-B histone acetyltransferase complex in histone turnover.
Verzijlbergen KF, van Welsem T, Sie D, Lenstra TL, Turner DJ, Holstege FC, Kerkhoven RM, van Leeuwen F.PLoS Genet. 2011 Oct;7(10):e1002284. doi: 10.1371/journal.pgen.1002284. Epub 2011 Oct 6.PMID: 21998594 [PubMed - indexed for MEDLINE] Free PMC Article
 
10.Interactions among Polycomb domains are guided by chromosome architecture.
Tolhuis B, Blom M, Kerkhoven RM, Pagie L, Teunissen H, Nieuwland M, Simonis M, de Laat W, van Lohuizen M, van Steensel B.PLoS Genet. 2011 Mar;7(3):e1001343. doi: 10.1371/journal.pgen.1001343. Epub 2011 Mar 24.PMID: 21455484 [PubMed - indexed for MEDLINE] Free PMC Article 

11.Gene expression profiles from formalin fixed paraffin embedded breast cancer tissue are largely comparable to fresh frozen matched tissue.
Mittempergher L, de Ronde JJ, Nieuwland M, Kerkhoven RM, Simon I, Rutgers EJ, Wessels LF, Van't Veer LJ.PLoS One. 2011 Feb 11;6(2):e17163. doi: 10.1371/journal.pone.0017163.PMID: 21347257 [PubMed - indexed for MEDLINE] Free PMC Article

12.The insulator protein SU(HW) fine-tunes nuclear lamina interactions of the Drosophila genome.
van Bemmel JG, Pagie L, Braunschweig U, Brugman W, Meuleman W, Kerkhoven RM, van Steensel B.PLoS One. 2010 Nov 24;5(11):e15013. doi: 10.1371/journal.pone.0015013.PMID: 21124834 [PubMed - indexed for MEDLINE] Free PMC Article

13.Volatile anesthetics modulate gene expression in breast and brain tumor cells.
Huitink JM, Heimerikxs M, Nieuwland M, Loer SA, Brugman W, Velds A, Sie D, Kerkhoven RM.Anesth Analg. 2010 Dec;111(6):1411-5. doi: 10.1213/ANE.0b013e3181fa3533. Epub 2010 Oct 1.PMID: 20889943 [PubMed - indexed for MEDLINE] Free Article

14.Systematic protein location mapping reveals five principal chromatin types in Drosophila cells.
Filion GJ, van Bemmel JG, Braunschweig U, Talhout W, Kind J, Ward LD, Brugman W, de Castro IJ, Kerkhoven RM, Bussemaker HJ, van Steensel B.Cell. 2010 Oct 15;143(2):212-24. doi: 10.1016/j.cell.2010.09.009. Epub 2010 Sep 30. Erratum in: Cell. 2011 Apr 1;145(1):160. PMID: 20888037 [PubMed - indexed for MEDLINE] Free PMC Article

15.Cross-species comparison of aCGH data from mouse and human BRCA1- and BRCA2-mutated breast cancers.
Holstege H, van Beers E, Velds A, Liu X, Joosse SA, Klarenbeek S, Schut E, Kerkhoven R, Klijn CN, Wessels LF, Nederlof PM, Jonkers J.BMC Cancer. 2010 Aug 24;10:455. doi: 10.1186/1471-2407-10-455.PMID: 20735817 [PubMed - indexed for MEDLINE] Free PMC Article

16.Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation.
Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I, Brugman W, Gräf S, Flicek P, Kerkhoven RM, van Lohuizen M, Reinders M, Wessels L, van Steensel B.Mol Cell. 2010 May 28;38(4):603-13. doi: 10.1016/j.molcel.2010.03.016.PMID: 20513434 [PubMed - indexed for MEDLINE]

17.One naive T cell, multiple fates in CD8+ T cell differentiation.
Gerlach C, van Heijst JW, Swart E, Sie D, Armstrong N, Kerkhoven RM, Zehn D, Bevan MJ, Schepers K, Schumacher TN.J Exp Med. 2010 Jun 7;207(6):1235-46. doi: 10.1084/jem.20091175. Epub 2010 May 17.PMID: 20479114 [PubMed - indexed for MEDLINE] Free PMC Article

18.BRD7 is a candidate tumour suppressor gene required for p53 function.
Drost J, Mantovani F, Tocco F, Elkon R, Comel A, Holstege H, Kerkhoven R, Jonkers J, Voorhoeve PM, Agami R, Del Sal G.Nat Cell Biol. 2010 Apr;12(4):380-9. doi: 10.1038/ncb2038. Epub 2010 Mar 14.PMID: 20228809 [PubMed - indexed for MEDLINE]

19.Recruitment of antigen-specific CD8+ T cells in response to infection is markedly efficient.
van Heijst JW, Gerlach C, Swart E, Sie D, Nunes-Alves C, Kerkhoven RM, Arens R, Correia-Neves M, Schepers K, Schumacher TN.Science. 2009 Sep 4;325(5945):1265-9. doi: 10.1126/science.1175455.PMID: 19729659 [PubMed - indexed for MEDLINE] Free Article

20.High-resolution mapping of heterochromatin redistribution in a Drosophila position-effect variegation model.
Vogel MJ, Pagie L, Talhout W, Nieuwland M, Kerkhoven RM, van Steensel B.Epigenetics Chromatin. 2009 Jan 29;2(1):1. doi: 10.1186/1756-8935-2-1.PMID: 19178722 [PubMed] Free PMC Article

21.Dissecting T cell lineage relationships by cellular barcoding.
Schepers K, Swart E, van Heijst JW, Gerlach C, Castrucci M, Sie D, Heimerikx M, Velds A, Kerkhoven RM, Arens R, Schumacher TN.J Exp Med. 2008 Sep 29;205(10):2309-18. doi: 10.1084/jem.20072462. Epub 2008 Sep 22.PMID: 18809713 [PubMed - indexed for MEDLINE] Free PMC Article

22.Multiple actions of lysophosphatidic acid on fibroblasts revealed by transcriptional profiling.
Stortelers C, Kerkhoven R, Moolenaar WH.BMC Genomics. 2008 Aug 14;9:387. doi: 10.1186/1471-2164-9-387.PMID: 18702810 [PubMed - indexed for MEDLINE] Free PMC Article

23.Ubiquitin E3 ligase Ring1b/Rnf2 of polycomb repressive complex 1 contributes to stable maintenance of mouse embryonic stem cells.
van der Stoop P, Boutsma EA, Hulsman D, Noback S, Heimerikx M, Kerkhoven RM, Voncken JW, Wessels LF, van Lohuizen M.PLoS One. 2008 May 21;3(5):e2235. doi: 10.1371/journal.pone.0002235.PMID: 18493325 [PubMed - indexed for MEDLINE] Free PMC Article

24.The T7-primer is a source of experimental bias and introduces variability between microarray platforms.
Kerkhoven RM, Sie D, Nieuwland M, Heimerikx M, De Ronde J, Brugman W, Velds A.PLoS One. 2008 Apr 23;3(4):e1980. doi: 10.1371/journal.pone.0001980.PMID: 18431470 [PubMed - indexed for MEDLINE] Free PMC Article

25.Dendrimer-mediated transfer printing of DNA and RNA microarrays.
Rozkiewicz DI, Brugman W, Kerkhoven RM, Ravoo BJ, Reinhoudt DN.J Am Chem Soc. 2007 Sep 19;129(37):11593-9. Epub 2007 Aug 29.PMID: 17725353 [PubMed - indexed for MEDLINE]

26.Oncogenic pathways impinging on the G2-restriction point.
Foijer F, Simonis M, van Vliet M, Wessels L, Kerkhoven R, Sorger PK, Te Riele H.Oncogene. 2008 Feb 14;27(8):1142-54. Epub 2007 Aug 13.PMID: 17700522 [PubMed - indexed for MEDLINE]

27.Somatic loss of BRCA1 and p53 in mice induces mammary tumors with features of human BRCA1-mutated basal-like breast cancer.
Liu X, Holstege H, van der Gulden H, Treur-Mulder M, Zevenhoven J, Velds A, Kerkhoven RM, van Vliet MH, Wessels LF, Peterse JL, Berns A, Jonkers J.Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):12111-6. Epub 2007 Jul 11.PMID: 17626182 [PubMed - indexed for MEDLINE] Free PMC Article

28.Reduced supportive capacity of bone marrow stroma upon chemotherapy is mediated via changes in glycosaminoglycan profile.
Zweegman S, Kessler FL, Kerkhoven RM, Heimerikx M, Celie JW, Janssen JJ, Huijgens PC, Drager AM, van den Born J.Matrix Biol. 2007 Sep;26(7):561-71. Epub 2007 Apr 19.PMID: 17521897 [PubMed - indexed for MEDLINE]

29.An shRNA barcode screen provides insight into cancer cell vulnerability to MDM2 inhibitors.
Brummelkamp TR, Fabius AW, Mullenders J, Madiredjo M, Velds A, Kerkhoven RM, Bernards R, Beijersbergen RL.Nat Chem Biol. 2006 Apr;2(4):202-6. Epub 2006 Feb 13.PMID: 16474381 [PubMed - indexed for MEDLINE]

30.Functional identification of cancer-relevant genes through large-scale RNA interference screens in mammalian cells.
Brummelkamp TR, Berns K, Hijmans EM, Mullenders J, Fabius A, Heimerikx M, Velds A, Kerkhoven RM, Madiredjo M, Bernards R, Beijersbergen RL.Cold Spring Harb Symp Quant Biol. 2004;69:439-45. No abstract available. PMID: 16117679 [PubMed - indexed for MEDLINE]

31.Induction of p53 up-regulated modulator of apoptosis messenger RNA by chemotherapeutic treatment of locally advanced breast cancer.
Middelburg R, de Haas RR, Dekker H, Kerkhoven RM, Pohlmann PR, Fuentes-Alburo A, Mohar A, Pinedo HM, Lankelma J.Clin Cancer Res. 2005 Mar 1;11(5):1863-9.PMID: 15756011 [PubMed - indexed for MEDLINE] Free Article

32.The deubiquitinating enzyme USP1 regulates the Fanconi anemia pathway.
Nijman SM, Huang TT, Dirac AM, Brummelkamp TR, Kerkhoven RM, D'Andrea AD, Bernards R.Mol Cell. 2005 Feb 4;17(3):331-9.
PMID: 15694335 [PubMed - indexed for MEDLINE]

33.FoxM1 is required for execution of the mitotic programme and chromosome stability.
Laoukili J, Kooistra MR, Brás A, Kauw J, Kerkhoven RM, Morrison A, Clevers H, Medema RH.Nat Cell Biol. 2005 Feb;7(2):126-36. Epub 2005 Jan 16.PMID: 15654331 [PubMed - indexed for MEDLINE]

34.Gene expression profiling in follicular lymphoma to assess clinical aggressiveness and to guide the choice of treatment.
Glas AM, Kersten MJ, Delahaye LJ, Witteveen AT, Kibbelaar RE, Velds A, Wessels LF, Joosten P, Kerkhoven RM, Bernards R, van Krieken JH, Kluin PM, van't Veer LJ, de Jong D.Blood. 2005 Jan 1;105(1):301-7. Epub 2004 Sep 2.PMID: 15345589 [PubMed - indexed for MEDLINE] Free Article

35.A large-scale RNAi screen in human cells identifies new components of the p53 pathway.
Berns K, Hijmans EM, Mullenders J, Brummelkamp TR, Velds A, Heimerikx M, Kerkhoven RM, Madiredjo M, Nijkamp W, Weigelt B, Agami R, Ge W, Cavet G, Linsley PS, Beijersbergen RL, Bernards R.Nature. 2004 Mar 25;428(6981):431-7.PMID: 15042092 [PubMed - indexed for MEDLINE]

36.Identification of differentially expressed genes in mouse kidney after irradiation using microarray analysis.
Kruse JJ, te Poele JA, Velds A, Kerkhoven RM, Boersma LJ, Russell NS, Stewart FA.Radiat Res. 2004 Jan;161(1):28-38.PMID: 14680399 [PubMed - indexed for MEDLINE]

37.Platinum(II)-based coordination compounds as nucleic acid labeling reagents: synthesis, reactivity, and applications in hybridization assays.
Heetebrij RJ, Talman EG, v Velzen MA, van Gijlswijk RP, Snoeijers SS, Schalk M, Wiegant J, v d Rijke F, Kerkhoven RM, Raap AK, Tanke HJ, Reedijk J, Houthoff HJ.Chembiochem. 2003 Jul 7;4(7):573-83.PMID: 12851925 [PubMed - indexed for MEDLINE]

38.Gene expression profiling predicts clinical outcome of breast cancer.
van 't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M, Peterse HL, van der Kooy K, Marton MJ, Witteveen AT, Schreiber GJ, Kerkhoven RM, Roberts C, Linsley PS, Bernards R, Friend SH.
Nature. 2002 Jan 31;415(6871):530-6.
PMID: 11823860 [PubMed - indexed for MEDLINE]

39.Two E2F sites control growth-regulated and cell cycle-regulated transcription of the Htf9-a/RanBP1 gene through functionally distinct mechanisms.
Di Fiore B, Guarguaglini G, Palena A, Kerkhoven RM, Bernards R, Lavia P.J Biol Chem. 1999 Apr 9;274(15):10339-48.PMID: 10187822 [PubMed - indexed for MEDLINE] Free Article

People working at the Genomics Core Facility

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Ron Kerkhoven

Head of the facility, Ph.D.

Experience

I was trained as a molecular biologist at the Free University of Amsterdam where I did my PhD on comparative neurobiology involving histology, anatomy and molecular biology on brains of insects, mollusks, reptiles and vertebrates.  As a post-doc at the NKI, I made monoclonal antibodies to dioxins in the lab of Erik Kriek and later to E2F transcription factors in the lab of René Bernards. There I got interested in transcription regulation resulting in the set-up of the KWF/NKI microarray facility in 2000 that has since developed into the Genomics Core Facility.  

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Arno Velds

Senior bioinformatician

Personal details

Experience

Immediately after obtaining my MSc at Wageningen University I started working as the bioinformatician at, what was then, the NKI Microarray facility. The microarray facility evolved into a next generation sequencing facility where I'm now responsible for all bioinformatic aspects like storage, processing and analysis. I like to work in close collaboration with a biologist and together squeeze answers from sometimes massive datasets.

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Iris de Rink

Bioinformatician

Personal details

Experience

In 2009 I graduated from the Hanze University of Applied Sciences in Groningen where I've studied bio-informatics. After my graduation I started to work as a bioinformatician at the Genomics Core Facility within the NKI. My main focus is to support researchers with the analysis of their sequencing data.

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Janneke Kruizinga

Technician, BSc.

Experience

Technician with DNAseq, CNVseq library preparation experience.

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Marielle Krete

Technician

Experience

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Marja Nieuwland

Head Technician, BSc.

Experience

I started working at the NKI in 2005, at that time still a microarray Facility which has now evolved to the Genomics Core Facility. As a head technician I am well experienced in all library preparation applications and operating the HiSeq and Miseq sequencing machines, but my main focus and interest lies in setting up and in the development of new applications. Beside my work in the lab I act as contact concerning questions about sample flow, experimental setup, time planning and financial aspects.  I like working at the Genomics Core Facility, contribute to all great experiments that are done within the NKI and working with the newest techniques.

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Roel Kluin

Bioinformatician

Personal details

Experience

After studying Biomedical sciences at the University of Amsterdam and a decade of autodidact Linux open source developer, bioinformatician at NKI's genetics core facility seemed the right position to include my skills and stay in touch with the wetlab. Handling the sequencer output and deducing from it answers, to each experiments variety of research questions, are challenges I like in my day to day work. I am specialized in capture bait design, the alignment pipeline and data management, single-, paired-end or whole genome data analysis. Including, but not limited to variantcalling and effect prediction.

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Shan Baban

Technician, BSc.

Personal details

Experience

Technician with RNA isolation skills, RNA amplification and Illumina hybridization experience, performing RNAseq, DNAseq, ChIPseq, DamIDseq and CNVseq library preparation, she is Illumina MiSeq operator.

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Wim Brugman

Technician, BSc.

Personal details

Experience

Technician with background in proteomics and microarray printing , performs RNA amplification and labeling, Illumina/Nimblegen hybridization, Perkin Elmer SciClone robot operator  and RNAseq library preparation from fresh frozen and FFPE material.

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Mandy Boer

Technician

Personal details

Experience

I studied Clinical Chemistry at Saxion University of applied sciences in Deventer. I carried out my internship in the group of John Hilkens, where I continued working as a technician. Initially I've generated monoclonal antibodies against cell surface antigens on human breast cancer. I was involved in biochemical en functional characterization of episialin (MUC-1). In more recent years I've been working on insertional mutagenesis and the identification of genes involved in mammary tumorigenesis like Eras and Rspo3. I'm familiar with various techniques like cell culture, molecular biology and protein analysis. An other major part of my work involves experimental animals

 

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