Manual NL BVTr for Labs - The Belgian Virtual Tumourbank
Contents
1. DNA RNA Proteins Corresponding normal tissue Serum Plasma gt Whole blood o Urine Manual BVTc for researchers version 3 UNDER REVISION 15 03 05 2013 Other Variable Name Control type Possible values Description Oncological variables Lesion type checkboxes Benign tumours indicates the lesion type of the sample in the local tumourbank Uncertain borderline tumours Insitutumours H Non tumourallesions gt mn EA meen guaranteed to have a standard terminology SOOO OSM amaran o o o E n eenn tumour localization Localisation primary T if meta ICDO code lists Anatomic localization of the primary tumour Laterality aro Left Anatomic side from which the sample was taken Unknown Morphology ICDO code lists i Morphology of the sampled tumour Degree of differentiation jr Well differentiated EN Tumour differentiation 1 4 for most tumours 5 8 for haematological tumours Be Moderately differentiated 2 aware particularly in case of haematological diseases that the differentiation grade Poorly differentiated 3 is not always completed by the tumourbank Undifferentiated anaplastic 4 T cell B o Brell 160 Nkeel 80 Unknown 9 MM checkboxes TNM code lists Pathological TNM The selected digit s represents tumours with a category starting with this digit TG e TNM code lists EN Clinical TNM The selected digit s represents tumours with a category starting with Manual BVTc for researchers version2. Fl 018 8 Overlapping lesion of colon D 018 9 Colon NOS a Continue with selection Manual BVTc for researchers version 3 UNDER REVISION 12 03 05 2013 Belgian Cancer Registry 4 4 Viewing search results 4 4 1 Result list At first the results will always be displayed in a list The total number of registrations is visible as well as the search criteria selected in the simple search page You can switch to extended view to see more parameters for the registrations You can click left of each registration to view the detail page You can download an excel version of this result list by clicking on Export From this selection you can refine your search with additional criteria or start a new search When you move with your cursor to a specific abbreviation like in sample type organ code and lesion code the description of that code will be displayed underneath the cursor SEARCH RESULT Your search returned 18 registrations displaying page 1 of 1 Primary malignant tumours 13 C44 Skin Sample Year Gender Age a oe Conservation Mode Tissue eas 2009 F 21 P C449 M8070 3 20 C Y Y View 2009 M 19 P C440 M8720 3 20 C N View 2009 F 17 P C441 M8743 3 20 C N View 2009 M 94 P C442 M8720 3 paraffin FFPE 20 C Y N View 2009 F 92 P C443 M 247 3 20 C Y Y View 2009 M 90 P C444 M8070 3 20 C Y Y View 2009 F 64 P C449 M8070 3 20 C paraffin FFPE Y N View 2009 F 64 P
3. C449 M8070 3 20 C paraffin FFPE Y N View 2009 M 62 P C440 M 720 3 20 C Y View 2009 M 62 P C440 M8720 3 20 C Y Y View 2009 F 60 P C441 M 743 3 20 C Y Y View 2009 F 60 P C441 M 743 3 20 C Y Y View 2009 M 58 P C442 M 720 3 20 C Y N View 2009 M 56 P C442 M 720 3 20 C N View 2009 F 56 P C443 M 247 3 20 C Y N View 2009 F 56 P C443 M 247 3 20 C Y N View 2009 M 54 P C444 M8070 3 20 C paraffin FFPE Y N View 2009 M 54 P C444 Ms070 3 paraffin FFPE 20 C Y N View Extended view Export Refine search criteria New search Manual BVTc for researchers version 3 UNDER REVISION 13 03 05 2013 Belgian Cancer Registry 4 4 2 Detail page The detail page displays all available variables of a registration You can navigate from one registration to another Previous Next and you can return to the search result list If you click on Display all registrations for this patient you can view all available samples from the same donor REGISTRATION DETAIL de Previous mb ext General variables Gender Female Laboratory a L444 Age 68 Reference ID El 415 Technical characteristics of the sample Sample ID T8147 Conservation delay El 0 30 min Sample year l 2008 Autopsy No Conservation mode El 50 C paraffin FFPE Available materials Tissue Oncological characteristics of the sample Sample type P Primary tumour Anatomic localization of the
4. 3 UNDER REVISION 03 05 2013 cM Manual BVTc for researchers version 3 UNDER REVISION 03 05 2013 this digit 17
5. Belgian Virtual Tumourbank Catalogue module BV Tc User manual UNDER REVISION Manual BVTc for researchers version 3 UNDER REVISION 03 05 2013 Belgian Cancer Registry CONTENT ar INRODIGNNN NN 3 25 GENERAL IINEORIVIA TON a o eS 3 3 CONCERT OF THE APPLICATION ocio cotas le too ias 3 o ser SE NE EEE EEG et 3 A A o NNN 4 3 3 Dataset and data content validation iii 5 BA ClASSINICALI sr NN ta tant a 6 3 5 Authentication via eHealth with eiD sese 7 4 WORKING WITHBV TC o o O 8 GS EE TN 8 A11 Systemreaqurenens ss 8 4 1 2 WepaddresBUTc hrs NT 8 4 1 3 Connection procedure eHealth with elb sss 8 A A AVIS ACI NE NE EE Sede 9 22 Sme Sears ets ate tata ole Ahk ene aati ae Eads 10 43 AdvareedSearn NNN 11 4 4 Viewing searehresults LE 13 TERRA 13 242 Dets A Se Ee orn PR Eee re 14 5 APPENDIX The different BVTc search variables cccccoocooooccnononcnononnoncnonnnncnononanonos 15 Manual BVTc for researchers version 3 UNDER REVISION 2 03 05 2013 Belgian Cancer Registry 1 INTRODUCTION This manual describes how to use the catalogue module of the Belgian Virtual Tumourbank BVTc The user should be able to retreive the samples he she is looking for using the available search criteria The concept of the BVT applications will be explained to give some insights to obtain better search results 2 GENERAL INFORMATION Belgian Cancer Registry BCR Biobank Project A
6. C300 Nasal cavity Anatomic laterality N A sample Morphology ICD 0 M8020 3 Carcinoma undifferentiated NOS Degree of differentiation N A Pathological TNM Clinical TNM h Return to list h Display all registrations for this patient Previous Next Manual BVTc for researchers version 3 UNDER REVISION 14 03 05 2013 Belgian Cancer Registry 5 APPENDIX The different BVTc search variables Variable Name Control type Possible values Description General variables Laboratory i Unique code identifying the originating laboratory communications pe the researcher and the Cancer Registry Female rm Age of the patient at the time of resection obtained by subtracting the sample date from the birth date Technical variables Sample ID text box unique and non identifying code of the sample within the local tumourbank Sample Year range year deduced from the sample date which is the date at which the sample was fixed the tumourbank Conservation mode checkboxes 20 o C indicates the various modes of conservation used for this sample in the local 800 tumourbank 120 C or colder Liquid nitrogen paraffin FFPE Other Conservation delay checkboxes 0 30min indicates the time elapsed between the removal from the patient and the fixation of 30min thesample Unknown Available materials checkboxes Tissue indicates which various types of materials are available in the tumourbank for the Cytology selected sample DNA
7. DNA samples Manual BVTc for researchers version 3 UNDER REVISION 11 i 03 05 2013 Belgian Cancer Registry Select codes In the advanced search tab there are 2 options to select codes for the sample localisation and for the histological diagnosis Oncological Variables Lesion type F Benign tumours 0 E Normal tissues E Non tumoural lesions E Uncertain borderline tumours 1 F In situ tumours 2 Fl Primary malignant tumpurs 3 E Metastatic ES Sample localisation Select codes 0 Laterality Fl Left AR Fl Odd Fl Unknown Histological diagnosis Select codes 0 When clicking this option a pop up window appears that allows you select the organs of morphologies of year interest In the example below a search is shown on sample localisation to retrieve colon samples By just entering the first letters e g colo and pressing the search button the application gives you all possible codes in this case of the colon After this the samples of interest can be indicated by checking them e g ascending colon and hepatic flexure of colon All selected samples will be queried if continue with selection is pressed Sample localisation E colo Results Select all selected codes N C16 2 Ascending colon 016 2 Ascending colon Y C18 3 Hepatic flexure of colon 15 3 Hepatic flexure of colon Fl C18 4 Transverse colon Fl 018 5 Splenic flexure of colon Fl 018 6 Descending colon El 018 7 Sigmoid colon
8. d ICD O classification International Classification of Diseases Oncology and the TNM of the UICC http www uicc org resources tnm These classifications are available in different versions depending on the year in which the tumour occurred Sample Year ICD O TNM TNM mme 1999 2000 2001 1998 TNM 5 cee TNM 6 E sen 0 3 2007 b a mo o 7 Manual BVTc for researchers version 3 UNDER REVISION 6 03 05 2013 Belgian Cancer Registry 3 5 Authentication via eHealth with elD The BVTc is a secured web application where the identity of the user will be verified authentication For this you need an electronic identity card To be able to use the elD services you should have installed on your computer e Acard reader Software to read electronic identity cards free via http eid belgium be fr Comment installer elD Quick Install click on corresponding icon You will need to know the PIN code of your elD to be able to login to the BVTc with your elD More information is also available on the eHealth website https www ehealth feov be fr acceder au portail ehealth eid Manual BVTc for researchers version 3 UNDER REVISION 7 03 05 2013 Belgian Cancer Registry 4 WORKING WITH BVTc 4 1 Start 4 1 1 System requirements This application will work best with Internet Explorer 8 or 9 or Firefox 5 or 6 4 1 2 Web address BVTc You can reach the catalogue
9. e advanced search section These two menus are always accessible via the links in the orange toolbar The results are displayed as a list that can be downloaded in excel format Mary Major Stichting Kankeregister logout Mary Major Stchting Kankaregster logost SIMPLE SEARCH SEARCH RESULT Select lesion type Your search retuned 6 registrations displaying page 1 of 1 Le Localisation C15 C26 Digestive organs 2 S E R C H Re Sample Date r gt Conservation Mode 19 04 2009 2 c4 W3 Z20 C parafin FFPE 20 04 2005 23 gt CAZ 5703 WC 07 08 2009 CAZ 203 WC 07 08 2009 CA2 5203 20 C C51 C58 Female genital organs 3 08 08 2009 20 C 08 08 2009 C42 70 3 20 C C69 C72 Central nervous system 3 ceececeecocecececoocoeesde 6 2011 Beiyan Cancer Registry Crested by MesttConzeg Version 1 0 REFINE Mary Major Stichting Kankerregister logout ADVANCED SEARCH General Variables SEARCH Technical Variables Sample ID Conservation mode 20 C E Liquid ritrogen Conservation Delay Autopsy Available materials Oncological Variables Lesion type Manual BVTc for researchers version 3 UNDER REVISION 9 03 05 2013 Belgian Cancer Registry 4 2 Simple Search On the simple search page you can visualize the distribution of the samples available in the virtual tumourbank according to the type of lesion and organ localisation using ICD O classification First select
10. m for publication to the catalogue If registrations are erroneous or identifiable towards the donor they will be rejected back to the lab for correction or inactivation deletion e All published registrations will be available in the catalogue for query The data will be codified i e it will not be possible to re identify the donor e Data are structured using a predefined dataset with minimal required fields Historical data i e data of samples from before 2010 have less required fields Manual BVTc for researchers version 3 UNDER REVISION 03 05 2013 Belgian Cancer Registry 3 3 Dataset and data content validation Data Element Variable Name Required Required for data before 2010 Visible in catalogue Laboratory O O E Creation date Update date Reference IDK SIN Birth date PX age pp yv TE ES Biopsy number KX Sample Date X only year O ee FONO a IA SA O ee DI O a pegree ot eran 7 A pT gt lt gt lt U wilh l A menn AM G Historical Data 1 PP Error Comment PP pe Manual BVTc for researchers version 3 UNDER REVISION 03 05 2013 Belgian Cancer Registry Every variable in the dataset has its own defined format and validation rules You can find more information about the variables in appendix 1 see 5 3 4 Classifications The tumours in the Belgian Virtual Tumourbank are classified according to the internationally acknowledge
11. module of the BVT by the following link https www virtualtumourbank be bvtc The links are available via the BVT website www virtualtumourbank be as well 4 1 3 Connection procedure eHealth with elD More information about elD see paragraph 3 5 Enter the url above in the web browser Click on Login Insert your elD in the card reader Click on identification via electronic identity card Select the appropriate certificate and enter your PIN code Choose the label Identification as a member of an organisation select the organisation of the Belgian Cancer Registry and click OK You will be forwarded to the homepage of the BVTc It is necessary to navigate throughout the application with the buttons within the application itself not those from your web browser Error connections can occur In this case it is advised to completely close your internet browser and to restart the connection procedure If the problem persists you can contact the Cancer Registry and mention the displayed ticket number if applicable ES When the application is not used for 30 minutes the session will automatically expire and you will be disconnected Manual BVTc for researchers version 3 UNDER REVISION 8 03 05 2013 Belgian Cancer Registry 4 1 4 BVTc Navigation The navigation in the BVTc is pretty simple and intuitive you can perform a quick simple search in the homepage or you can select other multiple criteria in th
12. raceli Diez Fraile Manager Biobank Araceli DiezFraile kankerregister org 02 250 10 12 Eva Van der Stock Data Manager Eva vanderstock kankerregister org 02 250 10 12 biobank registreducancer org biobank kankerregister org www virtualtumourbank be 3 CONCEPT OF THE APPLICATION 3 1 General The applications of the Belgian Virtual Tumourbank BVT are divided into 2 modules the BVTr and the BVTc Registration module Catalogue module BVTr BVTc for labs for researchers for BCR This manual contains information about the BVTc for researchers Manual BVTc for researchers version 3 UNDER REVISION 3 03 05 2013 Belgian Cancer Registry 3 2 Data flow of the BVT Local tumourbank manage registrations Tumourbank actions BCR actions BCR approve for publication Researcher view catalogue Each sample registration has a well defined state that defines which specific actions are allowed to be executed The BVTr application registration module will allow the local tumourbank and the BCR to populate the catalogue Some important principles e Each lab local tumourbank will be able to view all its registrations but will not be able to view another lab s registrations e Each lab is responsible for its own registrations e The BCR will be able to view all submitted registrations from all labs e The BCR will view the submitted registrations and approve the
13. s this page by clicking in the orange toolbar on Advanced search or by clicking Refine search criteria when you already performed a search action this last option remembers your previous search criteria ADVANCED SEARCH General Variables Laboratory E Reference 10 a Gender Male Female Age From 50 To Technical Variables Sample ID Sample year From To Conservation mode D 20 C D 80 C E 420 C or colder El Liquid nitrogen El paraffin FFPE Fl Other Conservation Delay El 0 30 min El 30 min El Unknown Autopsy Yes No e Available materials Tissue E Cytology VI DNA Fl RNA Fl Proteins Fl Corresponding normal tissue Fl Serum Fl Plasma El Whole blood Fl Urine Fl Other Oncological Variables Lesion type Fl Benign tumours 0 E Normal tissues E Non tumoural lesions Fl Uncertain borderline tumours 1 El In situ tumours 12 Fl Primary malignant tumours 3 Fl Metastatic tumours 6 Sample localisation Select codes 0 Laterality El Left Fl Right Fl Odd El Unknown Histological diagnosis Select codes 0 All the searchable variables are displayed on the screen Every filled or selected variable will be integrated in the search action with the AND logic between the parameters e g male AND from 50 years all males from 50 years andthe OR logic between the selected options within a parameter e g Tissue OR DNA in Available materials all tissue samples and all
14. the type of lesion then click in the tree structure on a plus sign or category name to expand the different levels Between brackets you find the amount of samples available for the given category or code Simply click on this number to go to the result list and view the individual registrations BELGIAN VIRTUAL TUMOURBANK Catalogue module Eva Martien Van der Stock Stichting Kankerregister logout SIMPLE SEARCH select lesion type Primary malignant tumours 3 700 results Make your choice here Benign tumours 0 a Uncertain borderline tumours 1 Localisation In situ tumours 2 Primary malignant tumours 3 C00 C14 Lip oral cavity 3 Metastatic tumours 6 C15 C26 Digestive organs Normal tissues C30 C39 Respiratory a ae C40 C41 Bones joints and articular cartilage 6 C42 Hematopoietic and reticuloendothelial systems 8 C44 Skin 18 C47 049 Connective and soft tissues C50 Breast 75 C51 C58 Female genital organs 23 C60 C63 Male genital organs 19 C64 C68 Urinary tract 216 C69 C72 Central nervous system 13 C73 C75 Endocrine glands 8 C76 Other and ill defined sites C77 Lymph nodes 17 C80 Unknown primary site 4 0 00 C HRL H Hal 0 0 0 0 2011 Belgian Cancer Registry Created by HealthConnect Version 1 1 1 Manual BVTc for researchers version 3 UNDER REVISION 10 03 05 2013 Belgian Cancer Registry 4 3 Advanced Search You can acces
Download Pdf Manuals
Related Search