Cyrillic 2.1
Contents
1. List Markers V Forenames IV Surname Date of Birth Sex Date of Death Age Father Mother Accession no Genetic Status Individual ID v Roman number Additional Information Sample number Phenotypes I Name Comments F Probe McKusick Number F Allele Names Enzyme F Allele Frequencies Chromosome band Relative Chromosome Position Marker Phenotypes Il Blood stored Separate allele fields I Blood location Marker Details in Heading Separate Columns DNA stored Cells stored DNA location Cells location Sample desired 52 Cyrillic 2 1 Pedigrees with Personal Data You can choose exactly which data to copy for selected or all individuals and can add a heading and column headings Note that in the above display the Marker details are greyed because there are no genetic markers set up for this family e Try out this feature by opening the file TUTOR4 FAM and choosing Edit Copy text e Check the boxes for which data is entered and don t forget to choose between the Selected or All radio buttons e Switch to your word processor or spreadsheet and paste in the tab delimited data Cyrillic 53 Pedigrees with Personal Data Number Forename Surname D O B D O D 1 David Jones 16 5 1919 12 8 1989 1 2 Helen Jones 5 5 1920 Ih Brian Jone2. Cyrillic 2 1 Getting Started Guide AP Benson Limited E mail support cyrillicsoftware com Soane Point Tel 44 0 8702 417019 6 8 Market Place Fax 44 0 8702 417023 Reading RG1 2EG United Kingdom End User License Agreement End User License 1 LICENSE 1 1 Cyrillic A P Benson Limited 2000 1 2 All rights in this product are reserved and exclusive distribution and marketing licenses have been granted to A P Benson Limited the Publisher This end user license agreement describes the rights and warranty granted to its customers by the Publisher By using the enclosed disk you the customer are agreeing to be bound by the terms of this agreement which includes the software license software limited warranty and hardware limited warranty 1 3 License The Publisher grants the customer and the customer accepts a non exclusive and non transferable license to use the Cyrillic software software so long as the customer complies with the terms of this Agreement 2 COPIES 2 1 The Publisher grants the customer the right to make copies of the software for back up purposes only The customer agrees to reproduce and incorporate the author s copyright notice on any copies It is expressly understood that such copies will not be used for any purpose except to substitute for the initial copy in the event that it is unusable 3 USE 3 1 In addition the license granted herein includes the right to move the soft
3. markers to it e Assign the disease to a family and enter the individual phenotypes e Create colour chromosome bars and manipulate the display e Perform a linkage analysis using the above data Cyrillic 55 Disease and Marker Data Markers Setup Entering the marker e Close Cyrillic and restart it from the Cyrillic 2 program item information This will give you a fresh clean environment to set up your data Examples of the data you will add are given in the Cyrillic 2 1 Tutorial environment which you can inspect later e Select Data Markers to display the Select Chromosome dialog box e Scroll down the list of chromosomes select X and click the OK button to display the Markers for Chromosome X dialog box Click the Yes button if asked to create a new file e Click the New button to display the Description of Marker dialog box 56 Cyrillic 2 1 Disease and Marker Data x IV List Individuals Sclocted Cancel fa e Include Column headings Include family ID Include Disease Individual Details Marker details Hep F List Markers IV Forenames IV Surname I Name J Comments IV Date of Birth Sex Probe McKusick Number Date of Death Age Allele Names Father Mother Enzyme Individual ID Accession no Allele Frequencies IV Roman number Genetic Status Chromosome band Additional Information Sample number Re
4. Viewer is displayed showing Disease Penetrances x iab Edi jcassnumbe NN no bo N mate D male Description 0 D00000 0 000000 1 000000 0 000000 0 000000 Disease penetrances Cyrillic 63 Disease and Marker Data e Click on the Allow Editing toolbar button and enter the following data for Class Number 1 EF Cyrillic Table View Table Edi avi 2 B classmumbe Nu Nb po N male p male Description NEN o 1 o 1 Default Disease penetrances e Click the Close toolbar button and confirm that you wish to commit the changes to return to ui the Disease Definition dialog box e Click the OK button to return to the Diseases dialog box then click its Close button to finish setting up the disease for the tutorial 64 Cyrillic 2 1 Disease and Marker Data Families Diseases and Markers Entering the Now that the Marker and Disease information has been entered we can assign it to sample family family information A e Click on the Open File toolbar button and open TUTOR2 FAM from the CYRILLIC 210 TUTORIAL FAMTREES directory io e Click on the Family Details toolbar button to display the Family Details dialog box Cyrillic 65 Disease and Marker Data Family details p x Family ID Number foppsi Family Name p ames Family Disease m Cancel Markers
5. WF va wa John James Judy Robert Ralph Richard Timothy Thomas Tony Anthony Smith Smith Smith White White White Young Young Young 2 2 1988 49 1989 9 6 1991 3 6 1991 24 5 1992 20 11 1003 2412 1992 9 3 1994 18 6 1996 H 189 0 185 195 i 189 179 185 179 189 185 187 I 185 b b a b b a b b a a b 76 Cyrillic 2 1 Hiding individuals and data Disease and Marker Data Now that the bars have been created you can toggle their display in the Display Format dialog box e Click on the Display Format toolbar button to show the Display Format dialog box e Uncheck the Barcodes check box While you are in the Display Format dialog box you can further manipulate the display For example e Uncheck the Surname Forenames Birth Date and Death Date check boxes e Change the Identifier Type to O000 9999 e Click the OK button to close the dialog and see the effect of these changes e Return to the Display Format dialog box and check the Barcodes check box again before continuing the tutorial You can show or hide all data using the Display Format dialog options but sometimes it is useful if groups of individuals or their data are hidden to focus on a subset especially in larger pedigrees Here are a few ways this can be achieved To hide spouses from the display e Choose Options Hide partners from display Cyrillic TT Disease and Marker Data e Repeat
6. and choose the file TUTOR2 PRE e You will be prompted for a second file choose TUTOR2 DAT The marker data for the remaining individuals is now displayed on the pedigree Cyrillic 71 Disease and Marker Data You ve already seen how you can view the marker data in the Table Viewer Let s now explore some Reviewing the other ways of viewing and editing the marker data for individuals Data e Double click directly on an individual phenotype to display the VNTR fragment sizes dialog box DXS297 or the Choose a marker phenotype dialog box DXS296 Note in particular the Phenotypes panel which lists the current parental and possible phenotypes You can select an alleles individually or choose one of the calculated possible pair e Click OK to close the dialog e Choosean individual and click on the Individual Phenotypes toolbar button to display the Individual marker data dialog box Note that you can also get to Note that you can also get to this dialog This dialog lists all the markers assigned to the family and the current box by clicking on the Markers phenotypes for the selected individual button on the Genetic Status pane in the Individual Data dialog e Click on a marker to display the VNTR fragment sizes dialog box box Note also that if more than one DXS297 or the Choose a marker phenotype dialog box DXS296 individual is selected
7. and his parents 14 Cyrillic 2 4 Disease and Marker Data David Jones 16 5 1919 12 8 1993 185 DE Wet Mna James David Brian Sarah William Gillian Bill William Cathy Jones Smith Smith White White Young Young 9 1 1968 3 6 1988 48 1969 3 2 1970 12 5 1970 8 11 1969 6 11 1972 189 191 187 b Wt v2 DE M4 Vs ve MT vs Iva John James Judy Robert Ralph Richard Timothy Thomas Tony Anthony Smith Smith Smith White White White Young Young Young 2 2 1988 49 1989 9 6 1991 3 6 1991 246 1992 20 11 1993 24 12 1992 9 3 1994 18 6 1996 189 185 195 189 179 185 179 189 185 187 185 b a b b a a b b b a b Now select James Jones 111 1 and choose Tools Create bars to create bars for him his sisters and his mother Finally choose John Smith IV 1 Robert White IV 4 and Timothy Young IV 7 in turn and choose Tools Create bars to create bars for their respective fathers and siblings 75 Cyrillic Disease and Marker Data i 1 2 David Helen Jones Jones 16 5 1919 12 8 1993 5 5 1920 185 187 185 7 5 I l This pedigree is saved in a B the file TUTOR4 FAM S I2 TES 1 4 I5 DE I7 James David Brian Sarah William Gillian Bill william Cathy Jones Smith Smith White White Young Young 9 1 1968 3 6 1968 48 1969 3 2 1970 12 6 1970 8 11 1969 6 11 1972 H 188 185 185 189 181 1285 179 187 185 H 188 b a b b b a b Iv V2 V3 M4 V5 v6
8. di Colour Pattern Help Quantitative Value a E Comments gt Creation Date 04 07 2002 Num Individuals in Family 20 cen ore Max Num Individuals 10000 Family drawn by e Type in the family ID Number and name as above 66 Cyrillic 2 1 x Disease and Marker Data Click on the Add Family Disease button to display the Add Loci dialog box Add loci E x Select one or more loci to add to the family list The maximum number is seven per family Oto palato digital Syndrome 1 OK Cancel Add locus Select Oto palato digital syndrome from the list and click the OK button Cyrillic 67 Disease and Marker Data e When prompted to use the default markers click on the Yes button e Add any other details you may want such as Creation date Family drawn by etc before clicking the OK button to close the Family Details dialog box These details are available to print on your drawing and do not show on the screen Various individuals are affected in this family and some are carriers for the disease Affection status e Select individual 111 1 and then lt SHIFT gt click individuals IV 1 IV 2 IV 4 and IV 7 and click the Affected button on the Symbol toolbar to the left of the pedigree Note that the tooltip will e display Oto palato digital Syndrome 1 e Select individual 11 2 and then lt SHIFT gt click the Carrier button on the Symbol to
9. files it is important to ensure that the working directory is set to a location which will not be accessed simultaneously by more than one user for example the users home directory on the file server or the PCs hard disk See Keeping family files in different sub directories for details of how to change the working directory If a user has a family file open it can be opened and read by other users but they cannot change it Six files are essential to run the program CYRILLIC EXE CYRILLIC HLP MOUSETRK DLL SPIN DLL WINEXEC DLL and TABLE DLL All should be kept in the same directory 18 Cyrillic 2 4 Network Installation Files Needed to Run Cyrillic Tutorials Part 3 Tutorials Guided Tour 4 Guided Tour Starting a program with a blank screen is always a little daunting so to familiarize you with Cyrillic s functions before you draw your own pedigrees we will take you on a guided tour using a complete pedigree before drawing one from scratch Step Look at a Family Tree e Windows 3 1 Choose the Cyrillic 2 1 Examples icon from the Cyrillic 2 1 program group e Windows 95 98 Millennium NT 2000 XP Select from the Start menu Start All Programs Cyrillic 2 1 Cyrillic 2 1 Examples e In Cyrillic open the file DEMOBARS FAM by selecting File Open Is 1 NEE SILI eee Cae IE rootbars You should see that all of the toolbar buttons shown above are now available Run your mouse curs
10. half on Genetic data entry and properties for the installed display as well as data import and export If you aren t interested in Cyrillic s disease program items to see how Bam this works For further and marker data handling capabilities you can skip the second half of the tutorial If details see chapter 8 of the you are you should start here and complete the whole tutorial Cyrillic User Guide e Click on the New Family toolbar button This will bring up the New Family dialog box Creating a new Family E 30 Cyrillic 2 4 Pedigrees with Personal Data Se x Family ID Number m Family Name B o d Just as the Individual data dialog Family Disease box is the hub for all an individual s al data so the Family Details dialog box is the starting point for adding family data such as diseases markers family name etc This is explored further in section 3 of the Cancel Markers Colour Pattern 411 Help tutorials Disease and Marker Data Quantitative Value and later in the reference section ot E 2 the User manual Comments v Creation Date Num Individuals in Family 0 Ee Uca Max Num Individuals 10000 Family drawn by Cyrillic 31 Pedigrees with Personal Data e Click on the OK button You are now ready to place the first individual The first Individual e To add the first individual click in the centre of the w
11. isn t technically possible it would otherwise e Click roughly 1 inch to the left of the existing twin to place the new twin left click be impossible for Cyrillic to for a male right click for a female switch the sex of a ROO d e Nowright click one of the twins to display the Relationship dialog again and click the Triplet button in the Multiples panel e Click roughly 1 inch to the left of the existing triplets to place the new triplet _left click for a male right click for a female Now convert one of the other existing siblings into a member of this multiple birth e Right click one of the triplets to display the Relationship dialog box and click the Quadruplet button e Instead of clicking in free space click on the sib closest to the other multiplets Note that we could have converted existing sibs at any stage of this process Cyrillic 37 Pedigrees with Personal Data mn d 6 Twins Monozygotic Triplets 38 Cyrillic 2 4 Pedigrees with Personal Data Quadruplets Cyrillic 39 Pedigrees with Personal Data You can also build up larger pedigrees by copy and pasting from other family files or even the same Copy and Paste file The individuals and their data are transferred completely It only remains for you to join the new segment to the growing pedigree We will illustrate this by replicating part of the pedigree within the same drawing e Drag a selection rectang
12. on whether your first individual is female or male The dialog box is cleared and the cursor changes from a pointer to the Relative Position cursor Cyrillic 33 Pedigrees with Personal Data e Click approximately 1 inch to the left or right of the first individual so that the male is on the left the conventional layout e Now add a single male child by right clicking either partner clicking the Son button Offspring panel and clicking the Relative Position cursor roughly 1 5 inches below the new parents Crooked Lines You may notice that the vertical line is crooked This is because the parents are an odd number of grid points apart and the descent line starts at the child on one grid point ending at the center of the marriage line between grid points This becomes more clear if you choose View Show grid To correct this e Select one of the parents hold down the lt CTRL gt and lt SHIFT gt keys together and press either the left or right cursor key This moves the selected individual to the left or right by one grid point and repositions the descent line accordingly You can also reposition the top of the descent line by grabbing it near the top with the left mouse button and dragging it to the left or the right Whilst a useful tool for fine tuning complex pedigrees it isn t appropriate here 34 Cyrillic 2 1 E Saving the drawing Adding more children Pedig
13. should now look more colourful with Cyrillics colour barcodes Marker data should be displayed to the side of the barcodes Cyrillic 25 Guided Tour NT N2 3 2 3 1 EA i E 2 3 s sme 200 You can edit the data in one of several ways You can either use the menus choose Data Individual l Js the toolbar or simply double click any data below a symbol on the drawing You can set the marker phenotypes set the crossovers on the barcodes edit the colours of the display and more Explore the different dialog boxes for marker and haplotype information 26 Cyrillic 2 4 Guided Tour You can also view the data in a spreadsheet type format e Click the Table view toolbar button to display the Table Viewer EF Cyrillic Table View xj Table Edit a 4 E erek 2 B Cyrillic 27 Guided Tour e Click on the Chrl4 tab at the bottom of the table to switch to the marker info e Close the Table Viewer by clicking the Close table toolbar button Step 4 Printing options Once you have entered and edited all your data you may want to print your pedigree The pedigree will print exactly as you have it displayed on the screen using whatever settings you have checked in the Format Display formats dialog box You can preview your drawing using the File Print preview command or Print Preview toolbar button When you select this a new window will
14. the Windows clipboard In addition tables of information about individuals and genetic markers can be placed into tables in reports etc also using the Windows clipboard The drawings can be printed on any Windows compatible printer with full annotation and control over the display Individuals and their descendants can be hidden from the drawing as can information about the genotypes of individuals Subsets of the pedigree can be printed on their own unconnected parents can be removed from the drawing they are always stored in a pedigree file in order to satisfy the requirements of linkage analysis programs Complete annotation of the pedigree the genetic markers and the genotype symbols can be added to a drawing Printouts are available of alphabetic and numeric lists of the individuals and information about them The program will also create circular drawings on one page It is possible to import pedigrees and marker data from standard sources such as MLINK pedigree files or GEDCOM files Output files for LIPED MLINK and CriMap can be easily set up and it is straightforward to run risk calculations using MLINK and a batch file created automatically by Cyrillic Cyrillic 2 1 7 Installing and starting Cyrillic The maximum family size is 10 000 persons with no limit on the number of generations There is a maximum of 150 markers per chromosome per family and 250 markers per chromosome A variety of marker types are available mo
15. the next symbol to the left notin the same sibship lt CTRL gt Right Arrow Select the next symbol to the right notin the same sibship Left Arrow Select the next symbol to the left Right Arrow Select the next symbol to the right Home Move the selection to the leftmost symbol in the current generation End Move the selection to the rightmost symbol in the current generation Escape Clear multiple selected symbols Insert Popup menu for selected symbols 12 Cyrillic 2 4 Installing and starting Cyrillic Shortcuts for If the lt SHIFT gt key is down when the arrow keys are used the newly selected symbol is added to any editing symbols group of symbols already selected Clicking on a symbol with the left mouse button and the lt SHIFT gt key down has the same effect lt CTRL gt A New individual s dialog lt CTRL gt B Date of birth and date of death lt CTRL gt D Dead alive lt CTRL gt E First names lt CTRL gt G Age gestation lt CTRL gt I Individual data dialog lt CTRL gt J Add relative lt CTRL gt K Genetic symbol lt CTRL gt L Change liability class es lt CTRL gt M Set marker phenotypes lt CTRL gt Q Symbol type pregnancy etc lt CTRL gt R Proband nota proband lt CTRL gt T Additional symbol types lt CTRL gt U Surname or last name Cyrillic 2 1 13 Installing and starting Cyrillic 3 Installing and starting Cyrillic Cyrillic is sup
16. to access dialog boxes and features These methods include toolbars program menus the Right Mouse Button shortcut menu and keyboard shortcuts In general only toolbar icons and program menus have been documented in this manual However the shortcut menu will also access many Cyrillic functions Note that the appearance of the shortcut menu depends on the area or component that is clicked See the Cyrillic User Guide for a list of keyboard shortcuts 4 Cyrillic 2 4 Installing and starting Cyrillic Part 2 Introduction Installing and starting Cyrillic 2 Introduction and overview Cyrillic is a program designed to display the most useful information about a pedigree for people working in human genetics clinical genetics genetic counseling and human molecular genetics Principal features The user draws pedigrees on the screen using a mouse and some simple dialogs Symbols are easily moved around the screen and their appearance altered with the program managing the details of the connections between individual symbols The pedigree data is displayed graphically and the user can select from a wide range of symbols including the option of adding letters as captions to symbols The editing of drawings is straightforward with simple selection of symbols and of regions of the drawing Text annotations may be placed anywhere on the drawing The main editing features are accessible from a toolbar and from floating menus for wh
17. to show the partners again To hide the affection status for all individuals e Choose Options Clear symbols displayed e Repeat to switch this option off To hide a group of individuals Drag a selection rectangle around 2003 2006 and their offspring 1003 1008 e Click the Hide Individuals toolbar button e Choose Tools Even spacing to clean up the display e Now reverse the process by choosing Edit Undo move menu and clicking the Hide Individuals toolbar button again To hide a group of individual s data e Draga selection rectangle around individuals 2000 2002 and their offspring 1000 1002 then lt SHIFT gt click individuals 2005 and 2006 and their offspring 1006 1008 e Choose Data Individual Hide show info 78 Cyrillic 2 4 Disease and Marker Data Note that you can hide or show an individual s data by E checking Hide Info in the Additionai Items panel of the Individual Data dialog box 1003 1004 1005 178 185 179 EY a Repeat the process for some or all individuals to show the data again Cyrillic 79 Linkage Analysis 7 Linkage analysis Running MLINK It is now straightforward to perform a standard linkage analysis with MLINK For more complex data you will have to have a full understanding of the LINKAGE package and alter the definitions of markers and disease loci appropriately e Open your last saved file or
18. 2 187 185 a b phenotypes offered by the Individual Marker Data I 185 a dialog See Chapter 12 of the User manual for more I2 189 179 a b details e Click the Commit Changes toolbar button and click the Close button to return tp the pedigree drawing e Todisplay the data on the pedigree click the Display Format toolbar button check the Markers and Marker Names Left Individual Only check boxes and click the OK button 70 Cyrillic 2 4 Disease and Marker Data The marker names and the genotypes you have entered for the first four individuals are now oe oe ee ee ts displayed on the pedigree LM 3 x Iv Identifier Sample number peel Horizontal x 100 Iv Surname W Barcodes Cancel dors 7 Markers Vertical X roo B IV Birth Date IV Haplotypes Symbol Width 53 Help I Death Date Marker Names A gt Default I Age Gestation Top R J With Alleles Default T Maiden Names T Left Individual ig _Use default C Show All muc z G Fatherless Only V Show DNA Blood Marriage Lines Symmetrical xi J Additional info Iv Kinship coefficients Date Format Day month year z Info Lines Identifier Type Use military date format 1 1 L 999 Importing To save you entering data for the remaining 16 individuals manually you can update your pedigree marker data from an MLINK file e Choose Data Update Update MLINK
19. ND MARKERS 65 DISPLAY AND PRESENTATION PART 2 74 7 LINKAGE ANALYSIS 80 RUNNING MLINK 80 NEXT STEPS 83 Cyrillic 2 1 vii About this Guide Part About this Guide About this Guide 1 About this Guide The Cyrillic CDROM contains full documentation of the Cyrillic 2 1 software This Getting Started Guide is intended to help you to get the software installed and to guide you through a first Cyrillic tutorial The full Cyrillic software documentation is contained in a pdf file which can be located using Windows Explorer or My Computer The CDROM also contains the Adobe Acrobat Reader software needed to read them The most current version of the Acrobat Reader can be found on the Adobe website at http www adobe com products acrobat main html Installing Adobe Acrobat Reader Installing Acrobat Reader Skip the installation of Acrobat Reader is you already have software capable of reading pdf files installed on your computer To install the Acrobat Reader software from the CDROM 2 Cyrillic 2 1 Locating Cyrillic Software Documentation About this Guide e Insert the Cyrillic CD into your CD ROM drive The installation routine should run automatically If it does not you must locate and run autorun exe e Open Windows Explorer or My Computer e Navigate to D where D is the name of your CD drive e Locate and double click autorun exe to run the installation The Cyrillic Software CD menu will open e
20. Pedigrees with Personal Data You may have noticed when in the Display Format dialog box that many features of the screen display are listed here Not only does it control which data items are displayed but also the date format the symbol scaling and width the format of the marriage lines and the Identifier Type Display Format e To avoid having to set these every time you enter a new pedigree you can save the settings by clicking the gt Default button e You can also apply these default settings to an existing pedigree by clicking the Use Default button You can change the fonts of different screen items by choosing Format Fonts More formatting SS xi First Line of Heading Change o ARIAL 10 Points Second Line of Heading Change ARIAL 10 Points Revert Descriptor Below Symbols Change Help ARIAL 10 Points Allele Descriptions etc Change ARIAL 10 Points Additional Information Change ARIAL 10 Points 48 Cyrillic 2 4 Annotations Print Preview ey Pedigrees with Personal Data And finally you can set line widths by choosing Format Line widths Note that the fonts and line widths aren t included in the user s default settings mentioned above Rather they are global settings applied to all opened or newly created pedigrees You can add general text to the pedigree in the form of annotations e Click the Annotation
21. Select Install Adobe Acrobat 4 Locating Cyrillic Software Documentation When you have Acrobat Reader software installed you will be able to read both the User Guide and Reference guide from the CDROM e Open Windows Explorer or My Computer e Navigate to D Manual where D is the drive letter of your CDROM drive e Locate and double click on the pdf file to access the full user manual o D Manual UserGuide pdf the full Cyrillic 2 1 User Guide The User Guide contains sections reproduced in this Getting Started Guide but Chapters 7 to 13 make up the bulk of the manual and explain how Cyrillic s tools and features work running the Cyrillic 2 1 3 About this Guide application using the interface pedigree drawing disease and marker data and linkage and risk analysis techniques Conventions used in Cyrillic documentation e Program menu commands are referred to as File Open for example meaning select Open from the File menu e Angled brackets are used to refer to keyboard characters For example lt Esc gt means press the Escape key lt Ctrl C gt means hold down the Control key whilst pressing C Alt F O gt means press the Alt key followed by F then O e LMBrefers to the Left Mouse Button and RMB refers to the Right Mouse Button menu For example RMB Parameters means click the right mouse button within the Model Viewer panel and select Parameters from the menu In Cyrillic there are typically several ways
22. TUTORA FAM MLINK is part of the LINKAGE suite of eu X di programs See Select File Export gt MLINK to display the Select loci for export dialog box MED o ep Guide for details of how to obtain and correctly reference it in any published work involving it s use 80 Cyrillic 2 1 Linkage Analysis e Select the disease locus and DXS297 and then click the OK button to display the MLINK Export dialog box ML INK Export File Name Directories mum e 2002 071 txt 2002 072 txt 2002 073 txt 2002 074 txt 20d193 1 txt 20d197 1 txt 20d19f 1 txt adobeweb log Cancel docume 1 di Help mymusi 1 progra 1 winnt Run program Rewrite locus file Use entered IDs C Append to pedigree file Rewrite pedigree file I View outfile dat e Change the directory to your LINKAGE directory making sure it contains MLINK EXE UNKNOWN EXE and MAKEPED EXE Cyrillic 81 Linkage Analysis e Enter the MLINK export file name The default is MLINK PRE e Select the Rewrite pedigree file radio button check the Run program Rewrite locus file and View outfile dat check boxes and Click the OK button to display the first in a series of MLINK parameter dialog boxes e When prompted enter the following data Recombination fraction 1 0 0 default Increment for rec fraction 0 1 Stop value for rec fracti
23. ate size families The printed page can include several items of information which are not displayed on the screen This is controlled from the Print options toolbar button e Click on the Print Options toolbar button and add some Family Details and a main heading then print your drawing e Click the Close button to clear the Print Preview window 50 Cyrillic 2 1 Cyrillic and your word processor Pedigrees with Personal Data Earlier in the tutorial we copied and pasted part of the drawing into the same Cyrillic window You can also copy and paste into other applications such as a word processor e Drag a selection rectangle around part of the pedigree and click the Copy toolbar button e Switch to your word processor or spreadsheet or load it if not running create a new document and paste in the selected individuals e To copy and paste the whole pedigree select just one individual the default state and click the Copy toolbar button Only the drawing elements are transferred when pasting into other applications You can copy and paste the data by choosing Edit Copy text to display the Copy to clipboard dialog box Cyrillic 51 Pedigrees with Personal Data I Heading v List Individuals Selected Include Column headings C All Individual Details Copy to Clipboard Include family ID Marker details Cancel F Include Disease Help lin
24. ath Date check boxes This shows an outline sketch of the Jones family into which we will add some personal information Cyrillic 41 Pedigrees with Personal Data a Boat 5 MER Cyrillic detects which date e Double click individual I 1 to display the Individual Data dialog box system your PC is using and accepts and formats dates e Enter Jones in the Surname last name and David in the forenames edit accordingly For example in boxes respectivel the USA May 16 would be 7 d entered 5 16 53 Note if Qu enter 53 for the year e Enter 16 5 19 and 12 8 93 in the Date of Birth and Date of Death edit a 1953 ond boxes respectively then click OK modifies the date accordingly Cyrillic uses full dates to avoid the Year 2000 problem The data you entered is now displayed on the drawing Note that the symbol for David Jones has changed to include a slash indicating Died Double clicking each individual in turn can get tedious especially if you are entering data in the same single field for a number of individuals e Drag a selection rectangle around individuals 1 2 11 1 and 11 2 and choose the Individual Data toolbar button Notice that the Next button is now active for Next Individual You can enter data for an individual and move to the next individual without leaving the dialog box 42 Cyrillic 2 1 The Table Viewer Pedigrees with Personal Data e Enter Helen Jon
25. c can import to generate a new family tree As data is added to the database it can be exported and used by Cyrillic to update the pedigree drawing Note that you can edit any displayed item of an individual s data by double clicking the item itself rather than the individual s symbol 46 Cyrillic 2 4 Pedigrees with Personal Data Display and Presentation Part Additional The Individual Data dialog box has an Additional Info field in the Identification panel for Information miscellaneous data e Double click an individual to display the Individual Data dialog then select the Identification radio button Pressing the Enter key Click in the Additional Information field and enter some text Up to 5 lines can will create new lines within the Additional Info Field be displayed on the drawing To exit the dialog from the keyboard Tab out oi the field and then press Enter e Click the OK button to close the dialog T e To show this text on the drawing click the Display Format toolbar button to bring up the Display Format dialog box and check the Additional Info check box e Choose how many lines of additional info you want to display and then click OK to close the dialog box An example of how you could use this feature would be to show or hide confidential information depending on who was to see the pedigree Cyrillic 4T
26. cally e You can add parents to the new spouse by right clicking the spouse and choosing the Both button from the Parents panel Now add a family of siblings to one of these new parents e Right click the parent and choose the Siblings button Family of panel to You can also add each display the Adding Family dialog again parent individually If you do you will notice that the er er i decent line for an individual e Add some brothers and sisters this time specifying a different order to the isn t drawn until the second boys first girls second default by clicking the Specify Sexes gt gt gt button to parent is added The chief reveal an extended Adding Family dialogue use of adding parents individually is to specify eran i isting individual e Choose the sex of each individual in order for example m f m m f for boy girl ee arias boy boy girl by clicking the appropriate radio button 36 Cyrillic 2 4 Pedigrees with Personal Data Multiple births Cyrillic can accommodate multiple births up to sextuplets 6 The general scheme is to add an offspring and then add a twin followed by successive multiplets up to the required number e Right click the male in the lowest generation to display the Relationship dialog and jou due choose one of the buttons from the Twins panel Note that the Multiples panel is afe SEM a male and vice versa inactive at this time Whilst this
27. cribed in detail in the Cyrillic User Guide page 64 e Cyrillic will work with Windows compatible printers and monitors A colour monitor is helpful but not essential to the operation of the program Keyboard Shortcuts There are four types of keyboard shortcuts used in Cyrillic Shortcuts to some of the menu items Shortcuts to aid in moving around the family Shortcuts to the buttons in the dialog boxes Shortcuts for symbol editing Cyrillic 2 1 11 Installing and starting Cyrillic lt CTRL gt N New family lt CTRL gt S Save family Menu Shortcuts lt CTRL gt 0 Open family file lt CTRL gt W Close family lt CTRL gt P Print family lt ALT gt X Exit program F10 Output to MLINK lt CTRL gt Z Undo symbol move lt CTRL gt X Cut selection to clipboard lt CTRL gt C Copy selection to clipboard lt CTRL gt V Paste clipboard lt CTRL gt A Select all symbols lt CTRL gt Add space lt CTRL gt F Find individual lt CTRL gt Remove space The window can be moved around the family by using the arrow and page movement keys Moving the cursor around They have the following actions the family Page up Move the window up by screen Page Down Move the window down by screen Up Arrow Select the next individual in the generation above Down Arrow Select the next individual in the generation below lt CTRL gt Left Arrow Select
28. e paid by the customer in respect of the defective material The Publisher or the authors or copyright holders shall have no further or other liability including without limitation in respect of damage to other property or in respect of any economic or consequential loss of whatever nature arising out of or in connection with the product or any part thereof or its use or application Should you have any questions concerning this license or this limited warranty or if you want to contact A P Benson for any reason please write to A P Benson Limited Soane Point 6 8 Market Place Reading RG1 2EG United Kingdom Copyright Disclaimer Trademarks Publisher Author Copyright Notice AP Benson Limited 2000 All rights reserved No part of this publication or the program Cyrillic may be reproduced transmitted transcribed stored in a retrieval system or translated into any language or computer language in any form or by any means electronic mechanical magnetic optical chemical manual biological or otherwise without prior written permission of the publisher This manual refers to version 2 1 of the program ISBN 0 9518236 2 0 Cyrillic User Manual 2000 AP Benson Limited make no representations or warranties with respect to the contents hereof and specifically disclaims any implied warranties of merchantability or fitness for any particular purpose All trademarks and registered trademarks are the property of their respec
29. es 5 5 20 for the first individual 1 2 and click the Next button Note that the Surname edit box is actually a list box from which you can choose previously entered surnames Note that the Prev button is also now active allowing you to review previously entered data e Enter Brian Jones 2 3 44 for the second individual and click the Next button e Enter Jane Jones 4 8 45 for the third individual and click OK Although this method of entry is productive it doesn t allow you to review data for many individuals simultaneously The Table Viewer lets you review and modify data for individuals in a spreadsheet format e Click the Table view toolbar button to display the Table Viewer Cyrillic 43 Pedigrees with Personal Data Cyrillic Table View Table Edit David Helen Brian Jane James David Sarah Gillian Cathy Brian John James Judy William Robert Ralph Richard Jones Jones Jones Jones Jones Smith White Young Smith Smith Smith Smith White White White Mihite When you first open the Table Viewer all available Cyrillic data fields are shown You can choose which fields to show and the order they are shown using the Table Viewer s Table Set upfields menu The field widths default to the widest text in a column and can be altered by dragging between the column header separators 44 Cyrillic 2 4 E Pedigrees with Personal Data To en
30. ession number which reflects the order in which individuals are entered the Pedigree number which can be used to reflect the individual s position within the pedigree and the ID number which 8 Cyrillic 2 1 Installing and starting Cyrillic indicates their ordering within the pedigree file Several numbering systems are available to indicate the pedigree or other orders These distinctions are made in order to protect the integrity of the data Cyrillic is handling Every effort has been made to give the program as much control over valid options as possible and to protect the user against entering obviously impossible or invalid data without affecting the flexibility required by the user New in Version 2 1 Table view of family information Symbol toolbar at left of window Up to 7 diseases per family Up to 7 quantitative loci per family Markers for more than one chromosome per family Update from MLINK or GEDCOM format files Extensions to GEDCOM format Keyboard shortcuts Enhanced risk calculation facilities for cancer families Cyrillic 2 1 9 Installing and starting Cyrillic New in Version 2 Open up to 10 family files at one time Copy and paste any part of drawing with clipboard Faster creation of outline pedigrees the program draws parents and siblings Better control of pedigree layout with improved handling of imported files Extensive use of colour Additional import export facilities with the GEDCOM for
31. fiers Cyrillic 21 Guided Tour Now look at how you can move the focus around the drawing and move individuals Notice that one individual on the drawing has a red box around it This indicates that it is the active or currently selected individual To select a group of individuals use the left mouse button and drag a box a Selection Rectangle Selecting and around the individuals you wish to select They will now each have a box around them Notice there moving is still one individual which has the main focus with the red box The others have a brown box individuals You can perform a sequence of operations on the selected group including moving their position on the drawing To move the group click the left mouse button over one of the selected individuals and drag to the new position You can do this repeatedly try it so you get used to how it works Then use the Edit Undo menu command to return to your starting point If you have done several moves in a row you can undo each of them in turn To deselect the group click elsewhere on the screen or on an unselected individual 22 Cyrillic 2 4 Zooming ala Guided Tour Experiment with the Annotation tool Just click anywhere on the drawing and a dialog box will let you enter your text You can set the colour font and style of your text from the Annotation dialog box You can move the text around the screen by dragging it with the left mouse bu
32. i ST The intention was to create a simple interactive method of entering pedigree data and family frees on the screen The program has retained this original focus while it has evolved through several versions and operating environments An early version of Cyrillic was described in a paper in the American Journal of Medical Genetics 1990 36 155 160 Work on the present Windows implementation started in 1991 and version 1 was released in 1993 The programs name was coined by the clinical geneticist Dr Mac Gardner who combined the name of the programmer with an interest he had in the Russian language Cyrillic 2 1 Contents Contents 1 ABOUT THIS GUIDE 2 INSTALLING ADOBE ACROBAT READER 2 LOCATING CYRILLIC SOFTWARE DOCUMENTATION 3 CONVENTIONS USED IN CYRILLIC DOCUMENTATION 4 2 INTRODUCTION AND OVERVIEW 6 PRINCIPAL FEATURES 6 OVERVIEW OF CYRILLIC 8 NEW IN VERSION 2 1 9 NEW IN VERSION 2 10 HARDWARE AND SOFTWARE REQUIREMENTS 10 KEYBOARD SHORTCUTS 11 3 INSTALLING AND STARTING CYRILLIC 14 DEFAULT INSTALLATION 16 4 GUIDED TOUR 20 STEP LOOK ATA FAMILY TREE 20 Cyrillic 2 1 vi Contents STEP 2 DATA ABOUT INDIVIDUALS 23 STEP 3 MARKERS DISEASES AND OTHER KINDS OF DATA 25 STEP 4 PRINTING OPTIONS 28 5 PEDIGREES WITH PERSONAL DATA 30 RELATIONSHIPS 35 PERSONAL DATA 41 DISPLAY AND PRESENTATION PART I 47 6 DISEASE AND MARKER DATA 55 MARKERS SETUP 56 DISEASES SETUP 61 FAMILIES DISEASES A
33. ich both the right and left mouse buttons are used to make selections Information about menus and toolbar buttons is displayed in a status bar Colour may be used to highlight various features of the drawing Genetic marker data with full documentation of the marker is defined once for all families which use that marker Thereafter phenotypes are selected from a list in a dialog box The program will haplotype families automatically and the user can draw patterned bars to represent haplotypes including crossovers and an indication of a region of uncertainty For certain types of families the program will create bars with crossovers as necessary Bars may be coloured as well as patterned 6 Cyrillic 2 1 Installing and starting Cyrillic Disease loci can have user defined penetrance classes or be defined as quantitative the details being in accordance with the requirements of the LINKAGE package For output to LIPED these disease details are translated automatically The user can select from four individual numbering systems which are automatically updated when new individuals arc added to the drawing Individual names dates of birth and comments are entered into dialogs and can be displayed on the screen There is complete control over line widths fonts colours symbol sizes scaling of the drawing and the information displayed about each symbol Pedigree drawings or parts of them can be added to word processed documents using
34. indow left mouse button for a male and right mouse button for a female e The Individual Data dialog box appears For now click the OK button to remove it The immediate appearance of this dialog can get in the way if you want to quickly sketch out a pedigree without adding any data You can toggle this feature by choosing Options Display new individual dialog e Doso now while we add some relatives to our lone individual Adding relatives e Add the first individuals spouse by right clicking the individual to display the Relationship dialog box 32 Cyrillic 2 4 Pedigrees with Personal Data Relationship 3 x I1 m Family of gt Parents Children Moth Heap When the Relationship chidren Mother He dialogue box is displayed Siblings Father many of the options are greyea Unconnected out The available options are Both those logistically permitted for the particular individual chosen Note that the Sibling and Partner Brother buttons are only active when you have right clicked an individual whose sex is unknown Sibling r Sibling Spouse Husband Sister Wife Partner Multiples iii iHi m Offspring r Twins Triplet o Monozygous Quadruplet Daughter Dizygous Quintuplet Mi itl Ni Child kind unknown Sextuplet e Click the Husband or Wife button depending
35. lative Chromosome Position Phenotypes Marker Phenotypes Blood stored DNA stored Cells stored Separate allele fields Blood location DNA location Cells location Marker Details in Heading Separate Columns Sample desired Cyrillic 57 Disease and Marker Data e Type in the name DXS297 and select the VNTR entered as allele length radio You may wish to enter button additional marker information e g You will notice that the Allele Names and Frequencies list box is now greyed out Chromosome Band as no alleles can be defined for VNTRs Enzyme Used and Probe Name In this e case Xq27 Xq28 Msp e Click the OK button to close the Description of Marker dialog box and return to and VOSAC but pas is the Markers for Chromosome X dialog optional The second marker is a Restriction Fragment Length Polymorphism RFLP with two alleles e Click the New button to display the Description of Marker dialog box 58 Cyrillic 2 1 Disease and Marker Data e Enter DXS296 in the Marker name box and choose the Allele names alterable radio button Description of marker Marker Name Numbered Alleles Allele Names Alterable Allele and Phenotype Names Alterable C VNTR Entered as Allele Length C System Shows Dominance Oxford Allele Description gt Letter Comments References etc Ch
36. le around part of the pedigree e g a family unit within the group and click on the Copy symbols toolbar button e Click the Paste Symbols toolbar button and then click roughly 1 inch to the right of the amp pedigree The individuals you copied are pasted into the new drawing To join the new section to the main pedigree e Right click one of the two individuals who will form the new relationship to Note You need to add each display the Relationship dialog box parent separately before the relationship is drawn on the e Choose the appropriate relationship and then click on the second individual screen When the Relationship dialog is displayed only valid relationships are available so you can see that what constitutes a valid new relationship for your key individuals requires some careful forethought 40 Cyrillic 2 4 Pedigrees with Personal Data Personal Data Entering Cyrillic can store a range of personal data such as names addresses birth dates etc along with personal individual and general annotation To explore this open the tutorial file TUTOR1 FAM information If you want further practice drawing pedigrees you can draw this family yourself It you do then before continuing with this tutorial you will have to choose the Tools Resequence menu And then the format display Format menu ana check the Identifier Surname Forenames Birth Date and De
37. mat for Complete specification of all information Automatic generation of recombinations in haplotype bars Batch printing Print preview with multiple or single page view Circular drawings Calculation of kinship coefficients and inbreeding coefficients Automatic recognition of consanguinity for partners Extended toolbars with status bar and floating help Hardware and software requirements Cyrillic 2 1 3 will run successfully on all recent versions of Windows 95 98 NT Millennium 2000 2000 Professional XP XP Professional The software will also run on Windows 3 1 or higher Originally released in 1993 Cyrillic 2 1 3 hardware requirements are easily met by any modern PC The standard minimum Windows hardware requirements must be met for your version of Windows 10 Cyrillic 2 4 Installing and starting Cyrillic For people with older hardware we should point out the following requirements and suggestions A two button mouse is required The program and associated files take up 4Mb of disk space A maths co processor is only necessary if you intend to do much serious work with one of the linkage packages and is not a requirement of the Cyrillic program itself A minimum of 2Mb of memory is required and 4Mb is recommended e The more complex the display with unusual fonts and symbols the slower redrawing will be However there are several things you can do to speed up interaction with the program and they are des
38. me and click OK to display the Disease Definition dialog box Cyrillic 61 Disease and Marker Data Oto palato digital Syndrome 1 Affection Quantitative C Risk locus Cancel Number of penetrance classes I Markers Frequency of Disease Allele fo 0002 Phenotypes Chromosome Male Mutation Rate 0 000000 Def colour Female Mutation Rate 0 000000 McKusick Number Help The Affection radio button is selected by default 62 Cyrillic 2 1 Disease and Marker Data Setting the allele frequency to 0 0002 ensures that for this genetically lethal condition the LINKAGE FASTLINK analysis programs will compute the probability of 0 666 that the mother of a child with OPD I is a carrier This is not critical to the analysis of this example but would be to any risk calculation Change the Frequency of disease allele value to 0 0002 Click the Markers button to display the Select Chromosome dialog choose X from the list and click the OK button to display the Select Markers dialog lt SHIFT gt click the DXS297 and DXS296 markers so that both are selected and click the OK button to display the Markers for Oto palato digital Syndrome dialog box Click OK to return to the Disease Definition dialog box Penetrances Now define a single penetrance class for Oto palato digital Syndrome 1 e Click on the Phenotypes button The Table
39. n detail Explore it at your leisure as you become more familiar with Cyrillic and refer to it when you aren t sure of a feature If you still cant do what you want you can post e mail to the cyrillic user cherwell com mailing list which has many experienced subscribers You can also get technical support by sending e mail to the addresses listed for your region at the front of this manual Cyrillic 83
40. of the manual Tutorial 16 Cyrillic 2 1 Cyrillic 2 1 Breast Cancer Example Cyrillic 2 1 Examples Cyrillic 2 1 Help Cyrillic 2 1 Shortcuts Read Me Remove Cyrillic 2 1 Installing and starting Cyrillic Example Sets the working directory to lt InstDir gt BRCANCER and can be used to open family disease and marker data file examples It also automatically assigns Breast Cancer to newly created families enabling them to be analyzed using MLINK and the installed BrCa module Sets the working directory to lt InstDir gt EXAMPLES and can be used to open the more general example family disease and marker data files in this directory A comprehensive on line help file Brief descriptions of Cyrillic s keyboard shortcuts Important last minute information Please do read it An uninstaller that will remove the installed files but not newly created files Cyrillic 2 1 17 Installing and starting Cyrillic Cyrillic can be installed on and run from a network server provided your system Manager ensures that no more copies of the program are run simultaneously than there are licenses Disease and marker data files can be set to feed only by the system manager and Cyrillic will read them and not attempt to make any changes to them However there is no provision for handling multi user read write access to the marker and disease files If you wish to allow more than one user to maintain copies of these
41. olbar a To assign a heterozygous affection status e Select individual 111 3 and then lt SHIFT gt click individuals 111 5 and 111 7 e Click the Individual Data toolbar button to display the Individual Data dialog box and click the Genetic Status radio button e Choose the Heterozygous genetic symbol for each individual in turn cycling between them by pressing the gt Next button e Click the OK button to close the Individual Data dialog box 68 Cyrillic 2 4 Disease and Marker Data Entering the Now we will assign marker phenotypes to each of the individuals in the pedigree The quickest way to marker data enter data manually is to use the Table Viewer e Choose Data Show table to display the Table Viewer You will notice that there are now two sheets in the workbook E Table Edit See 4 amp eve 8j Ped Num FamibyID Mother Father Fitstname Sumame Knomn as Othernames Maiden name Sex Bem Died a o po David m 16 5 1919 12 8 1993 Helen f 5 5 1920 1 Brian m 2 3 1944 e Click the Chr X tab to display the family markers for the X chromosome Click the Allow Editing toolbar button and enter the following marker data Cyrillic 69 Disease and Marker Data ID Number DXS297 DXS296 dese UIE quickest means of data A entry the Table Viewer l1 185 a doesn t have the level of configuration of individual I
42. on 0 4 e When asked if you want to enter any more values click the NO button default The analysis now proceeds and the results are saved in the file OUTFILE DAT in the LINKAGE directory The file is opened automatically in NOTEPAD Windows default text editor e After reviewing the results quit from NOTEPAD e To analyze the second marker against the disease locus repeat the MLINK export command If a file already exists with your chosen export file name you will be prompted to check if you want to overwrite it If you want to overwrite it press OK to continue or Cancel to enter a new file name Cyrillic Creates a batch file in the working directory called RUNML BAT This runs the MAKEPED EXE UNKNOWN EXE and MLINK EXE programs in turn If you are using LINKAGE v5 20 or greater it also runs the LOOPS EXE program The RUNML BAT file remains after the analysis so you can view it if you are curious about it s operation 82 Cyrillic 2 1 Linkage Analysis Next Steps This completes the tutorial There are many other options available for drawing and annotating pedigrees or for preparing output to LIPED CriMap SIMWALK or GEDCOM However you have covered most areas in outline and should be able to confidently draw your own pedigrees and enter disease and marker data The reference section in the Cyrillic 2 1 3 User Guide on the CDROM covers all aspects of the program i
43. open showing the pedigree as it will appear on the printed page If your drawing is larger than a single page it will display the number of pages required to print at the current scaling using dotted lines to show page margins You can set the scaling here using the toolbar option showing percentages You can shrink the drawing to fit on a single page or print a circular drawing by clicking on the relevant toolbar button 28 Cyrillic 2 4 Guided Tour SN E k A 3 LED o EA ec we Ww l lt o oO A I po x v P4 P4 Ne I JA ia N Er Ez 2 u IV Note that genetic information is not shown on the circular drawing The print and display settings can be controlled from the Print Preview window In the demo version a banner will be displayed across your printout Cyrillic 29 Pedigrees with Personal Data 5 Pedigrees with personal data For the rest of the tutorial you will open the program using either the Cyrillic 2 l program item when creating your own files or the Cyrillic 2 1 Tutorial program item if you want to open one of the 4 supplied tutorial files A New Pedigree You can use different data and family directories by Now that you have an overview of Cyrillic the remainder of the tutorial will take you ew ee rs through pedigree drawing and data entry from scratch The first half concentrates on Oyrillic ini files Look at the personal data entry and display and the second
44. or over the toolbar without pressing a button pausing over each of the buttons note the tool tips which briefly describe the function of each icon Towards the left of the toolbar the tools control standard Windows functions such as Save Copy and Paste To the right of this are general settings for the family such as Family Details and Markers In the middle are display settings and zoom controls The remainder of the tools control the properties of an individual e g the proband and the other members of their pedigree 20 Cyrillic 2 4 Display options Guided Tour Note if you are using a VGA monitor 640 x 480 resolution a truncated version of the toolbar is displayed omitting 1 the clipboard buttons cut copy paste 2 the button Show Descendents Only 3 the button Hide Individual 4 the button Show All and 5 the Help button On the drawing you will see that each individual e g the proband and the other members of their pedigree Can have a lot of data associated with them All this data can be shown or hidden from the drawing as you need Clicking on the Display Format button shows a dialog box where you can control what is displayed on screen Click on the Haplotypes Barcodes and Markers check boxes to deselect these i e hide them from the display Then click OK You will see that the drawing is simplified to show only the individuals with their identi
45. plied on a single CDROM To install Cyrillic e Insert the distribution disk in your CDROM drive e n Windows 3 1x Select File Run and type a autorun exe e n Windows 95 98 Millennium NT 2000 XP The software should start automatically when you put the CDROM into your computer Ifthis does not happen e Select Run from the Start menu e Intherun open dialog box type D Nautorun exe where D is the drive letter of your CDROM drive e Select Install Cyrillic 2 1 3 and click Open in the file download dialog box SETUP will guide you through the installation process and create a Program Group called Cyrillic 2 1 containing a number of program items The default installation directory is C NCYRILLIC 210 but you can change this The installation of Cyrillic requires less than 4Mb of disk space including all sample files The minimum installation takes about 1 7Mb of disk space The SETUP program will check that your destination disk contains at least this before copying any files 14 Cyrillic 2 1 Installing and starting Cyrillic Upgrading Cyrillic Cyrillic version 2 1 x is installed into a different directory from version 2 0 x C CYRILLIC and version 1 x C FAMTREES It is strongly recommended that you don t change the install directory to that of a previous version Copy any existing family and data files into the new directory structure after installation and before using the new version File type Copy
46. rees with Personal Data When working with any software application you should get into the habit of saving your changes every five minutes or so e Save your work by clicking on the Save Family toolbar button The first time you press this button the Save as dialog is displayed The default filename is taken from the family name or Family ID number if no name is entered Subsequent presses will update the same file Choose File Save as 4 if you want to save a copy elsewhere or under a different name Relationships You can add further individuals to a sibship in the same way as you added the first offspring e You can right click either of the parents and choose an offspring e You can right click one of the existing offspring and choose a sibling In each case you have to click on the drawing where you want the new individual to be place Cyrillic 35 Pedigrees with Personal Data Sketching out a large pedigree one individual at a time can be very tedious Cyrillic can add parents Adding families a spouse and children up to 15 or parents and siblings up to 15 in a single step in one step e Right click the second offspring to display the Relationship dialog box and click the Children button Family of panel to display the Adding Family dialog e Enter 1 boy and 3 girls in the appropriate edit boxes and click the OK button The new family including the spouse is drawn automati
47. romosome Band Relative D Chromosome Position McKusick Number Enzyme Used Probe Name Cancel Phenotypes Allele Names and Frequencies Number of Alleles P Cyrillic 59 Disease and Marker Data The frequencies of the alleles a and b are 0 87 and 0 13 respectively e Enter these names and values by clicking on the names in the Allele names and Frequencies list box in turn to display the Details of Allele dialog box E Loci in the file e Click the Reposition button to display the Marker Position dialog box mus Bro and select DXS297 from the list box to place the new marker after it in the list The Markers for Chromosome X dialog box is now displayed Endat fie Help e Click the OK button to display the Select Chromosome dialog box and finally click the Close button in this dialog to complete the marker WDR definition at ine nis sed ls auke Weto follow Note if the Rel Pos Cursor is showing press lt ESC gt to cancel the placement of an individual at this stage 60 Cyrillic 2 4 Disease and Marker Data Diseases Setup Entering the e Select Data Diseases to display the Diseases dialog box and click the New button to disease display the New Disease dialog box information New disease Enter new disease name Oto palato digital Syndrome 1 caca e Enter Oto palato digital Syndro
48. s 2 3 1944 W 2 Jane Jones 4 8 1945 Wh James David Jones 9 1 1968 IIl 2 Brian Smith 3 6 1968 Ill 3 Sarah Smith 4 8 1969 l 4 William White 3 2 1970 Ill 5 Gillian White 12 6 1970 Ill 6 William Young 8 11 1969 Hl 7 Cathy Young 6 11 1972 IV 1 John Smith 2 2 1988 IV 2 James Smith 4 9 1989 IV 3 Judy Smith 9 6 1991 IV 4 Robert White 3 6 1991 IV 5 Ralph White 24 5 1992 IV 6 Richard White 20 11 1993 IV 7 Timothy Young 24 12 1992 IV 8 Thomas Young 9 3 1994 IV 9 Anthony Young 18 6 1996 Further display options are explored in a later part of the tutorial Display and Presentation 2 These deal with individual data display and hiding They can be followed without having to follow the disease and marker data entry sections 54 Cyrillic 2 1 Disease and Marker Data 6 Disease and marker data Now that you have drawn a pedigree and entered personal data you can enter clinical or research data in the form of disease and marker information and phenotypes First you have to enter the disease and marker information Then you assign the disease and marker phenotypes to individuals Marker and disease information is held independently of any particular family so any changes made will affect all families which use it In the second half of the tutorial we will e Enter marker information for X chromosome markers DXS296 and DXS297 e Enter disease information for Oto palato digital Syndrome assigning the previously entered
49. st of which have up to 40 alleles with the exception of the Allele names alterable type which has a limit of 150 alleles Projects or families grouped by disease can be stored in separate directories to allow separate definitions of disease loci and genetic markers A README TXT file will be provided on the distribution disk if there have been any changes to the program since this manual was printed It will contain details of any new developments or enhancements and may also contain supplementary information concerning the use of other programs like MLINK EXE DLLs and technical notes Please refer to this file for the latest information concerning Cyrillic and for any modifications to the documentation Overview of Cyrillic All new individuals in a pedigree apart from the first are assigned by selecting clicking On a symbol for a first degree relative who is already in the drawing and then selecting the relationship of the new person or persons in a dialog box For example to add a husband for person A click on the symbol for A with the right mouse button Select Husband from the dialog box and when the dialog disappears click the left mouse button with the pointer on the screen position where you want the husband s symbol to appear The program will set up the individuals records to reflect your choice Connections can be unmade using buttons in the individual and spouse dialog boxes Note that a distinction is made between the acc
50. ter more data click the Allow Editing toolbar button Enter data for the following individuals Wha Wh Il 3 Il 4 Il 5 Ill 6 Hl James David Sarah Gillian Cathy Brian William Bill William Jones Smith White Young Smith Young Young 9 1 1968 4 8 1969 12 6 1970 6 11 1972 3 6 1968 8 11 1969 4 3 1970 Note that William Young is known as Bill and Cyrillic has a separate field for this e When all this data is entered click the Commit Changes toolbar button Depending on how the Table Viewer overlaps with the main Cyrillic window you can see that the drawing is updated as you commit the changes Close the Table Viewer by clicking the Close Table toolbar button Cyrillic 45 Pedigrees with Personal Data You can also add data to a pedigree with a data file in GEDCOM or MLINK format The data file must have the same family structure and not have any additional individuals e Try this feature by reopening TUTOR1 FAM and choosing the Data Update gt Update GEDCOM menu choosing TUTOR1 GED when prompted for an update file e Choose Data Show table to review the newly imported data e Click the Close Table toolbar button to return to the drawing window A typical for this feature could be a custom database used to store family data The first step for a new family might be to export a skeleton GEDCOM file from the database which Cyrilli
51. tive companies Cyrillic was written by Cyril Chapman Professor John Edwards is acknowledged for his contribution to the development of the haplotyping algorithm Richard Houlston is acknowledged for his assistance with risk calculations Cyrillic 2 1 is published by AP Benson Limited E mail enquiries cyrillicsoftware com Soane Point Tel 44 0 8702 417019 6 8 Market Place Fax 44 0 8702 417023 Reading RG1 2EG United Kingdom Cyrillic 2 1 iii Copyright Notice E mail support queries should be sent to support cyrillicsoftware com Technical Support You may find an answer to your question on the CyrillicSoftware web site http www cyrillicsoftware com support techsupport htm To log a support question by telephone please call our UK office directly on 44 0 8702 417019 between the hours of 9 30 and 17 30 UK time Monday to Friday inclusive excluding UK public holidays Telephone calls will be logged in our support system and you will be contacted by e mail fax or telephone with a solution or a request for more information Note on the Developer Copyright Notice For some years Senior Lecturer in Clinical Genetics at the University of Auckland School of Medicine Dr Chapman moved to the Churchill Hospital Oxford in the summer of 1993 where he is now Clinical Director in the Department of Clinical Genetics Cyrillic has its origins in a program developed by Dr Chapman from 1987 to 1989 for the Atar
52. to FAM files INSTALL DIR NFAMTREES DAT files INSTALL DIR gt DATA where INSTALL DIR is by default CYRILLIC 2 1 0 This is only a recommended method of organising Cyrillic files for detailed information see chapter 8 Configuring Cyrillic and Keeping family files in different sub directories in the Cyrillic User Guide NOTE Once saved in the new version files are incompatible with previous versions Cyrillic 2 1 15 Installing and starting Cyrillic Default Installation File Edit View Favorites Tools Help ebak gt fy Qsearch GyFolders C Um GE X A Ea Address a C Documents and Settings All Users Start Menu Programs Cyrillic 2 1 BI Cyrillic 2 1 Breast Cancer Example e BI Cyrillic 2 1 Examples Cyrillic 2 1 BM Cyrillic 2 1 Help BP Cyrillic 2 1 Keyboard Shortcuts Select an item to view its description BP Cyrillic 2 1 Tutorial See also BR Cyrillic 2 1 i F Read M My Documents ead Me My Network Places Remove Cyrillic 2 1 My Network Places The full Cyrillic 2 1 installation creates the following Program items Note lt InstDir gt is c CYRILLIC 210 in the default installation The main program item which uses the default working directory of lt InstDir gt and should be used for Cyrillic 2 1 new files Sets the working directory to lt InstDir gt TUTORIAL and can be used to open family disease and Cyrillic 2 1 marker data files used in the Tutorial section
53. toolbar button Note that the cursor has changed to an beam e Click on the drawing where you want to place the annotation The Edit Annotation dialog is displayed where you can enter text You can also format the annotation from this dialog box setting justification font and colour e Try setting your text to Anal 48 Centred in Red and then click OK The annotation is now displayed on the pedigree You can move it by grabbing it with the mouse and dragging it To edit the text double click it and to delete it click it once and press the Delete key Print Preview lets you control the final output prior to printing For example if you are printing a large pedigree over many pages you can move the pedigree in relation to page breaks e Click on the Preview Printout toolbar button The screen changes to show a representation of the pedigree as it will appear on paper and a new toolbar appears Cyrillic 49 Pedigrees with Personal Data Four of the toolbar buttons control the way the pedigree is displayed Bjo afe e Select the first and you see the pedigree spread across as many pages as are necessary to print e The second shows just the first page and is intended to allow the various header options to be placed as desired e The third shrinks the pedigree so that it will fit on a single printed page e The fourth displays the pedigree in a circular format These last two options only work sensibly on moder
54. tton and edit it by double clicking on it Use the Zoom In and Zoom Out features by using the magnifying glass Button on the toolbar or View menu items Note that these settings do not affect the printed size of the drawing They are simply to show the family in more or less detail on the screen We will look at the print preview options later Step 2 Data about Individuals Cyrillic is also used for managing and reporting clinical and genetic information Using the same example file double click on an individual on the drawing or click on the Individual data toolbar button with the individual highlighted This opens a dialog box from which you can edit all the information about that individual relevant to Cyrillic This dialog box has two main sections an upper part which does not change and a lower part from which you can move through subsets of data by use of the radio buttons e g Sex is shown in the Identification pane Cyrillic 23 Guided Tour Surname x Date of Birth e Forenames Date of Death Cancel Maiden name ba Age Gestation Help Individual ID ll Pedigree Number II 2 Father 1 3 QE Proband gt Next roban Not a proband M RE Next Individual ex Num individuals fi Previous Individual lt Prey Identification Genetic Status Additional Items Samples Le Genetic Symbols Clear symbol Liability Class Colour Additional S
55. ware from one computer to another provided that the software is used on only one computer at a time and that two people will not use the program at the same time on different computers 4 SECURITY 4 1 The customer agrees to secure and protect each disk the documentation and copies thereof from copying except as permitted above or from modification and shall ensure that its employees or consultants do not copy or modify the product Cyrillic 2 1 i End User License 5 OWNERSHIP 5 1 The Publisher represents that it has the right to grant the licenses herein granted 6 LIMITED WARRANTY 6 1 6 2 6 3 Whilst all reasonable efforts have been made to test the software and user manual prior to first publication the authors and Publisher welcome corrections being brought to their attention The liability of the Publisher in respect of any defect error or omission in the disk user manual or software defective material and in respect of any breach of warranty or condition is limited to the purchase price paid by the customer The Publisher shall have no liability whatsoever arising out of any defect error or omission or breach of warranty or condition unless the customer shall have returned the defective material to the Publisher within 90 days of the date of purchase In that event the Publisher shall as requested by the customer either replace the defective material without charge or refund the purchase pric
56. when the Individual Phenotypes toolbar e Click OK to close the dialog box button is clicked you get the option of cycling through the phenotypes of 3 all or selected individuals in turn e You probably haven t saved your work for a while so choose mie seite HU uses wifi File Save as and save the file under a different name care 72 Cyrillic 2 4 Disease and Marker Data Finally to confirm that the data displayed is correct here is a complete list of all phenotypes entered for this family ID number DXS297 DXS296 I 185 a 1 2 187 185 a b I1 185 a I2 189 179 a b Td 189 b I2 195 a I3 185 189 a b I4 191 b Ill 5 185 179 a b IN 187 a H7 185 189 a b IV 189 b IV 2 185 b IV 3 195 189 a b IV 4 179 b IV 5 185 a IV 6 179 b IV 7 189 b IV 8 185 a IV 9 187 185 a b Cyrillic 73 Disease and Marker Data You can check this by looking at the Table View Chr X tab e Choose Table Sort by and select Pedigree number to compare the values Display and Presentation Part 2 Now that all the disease and marker data has been entered we can create colour chromosome bars Chromosome bars e Open TUTOR3 FAM or your last saved tutorial file e Choose Tools Form haplotypes e Select Brian Jones 11 1 and choose Tools Create bars to create coloured chromosome bars for Brian
57. ymbols Clear symbol S Style Multiple Pregnancies Singleton Test status hearsay Hide Info pregnancy outcomes Normal M e All Markers Unknown Markers 24 Cyrillic 2 4 Displaying marker data Guided Tour The Individual Data dialog box is like a form and through it you can use Cyrillic as a database for individuals within a family or a collection of families If you select a group of individuals and then edit individual data records you will find that you can cycle through a group of records using the Next and Previous buttons in the dialog box This is a quick way of making a change to a group of records Enter some sample data for names and dates of birth in a group of individuals Cyrillic makes use of information that you enter in a variety of ways When you enter data about an individual e g Names Date of Birth Genetic Symbol etc some or all of this information can be displayed on the drawing Any genetic symbols will automatically be displayed The display of all other information can be controlled using the Format Display format menu option as mentioned in Step 1 above and checking the relevant boxes Step 3 Markers Diseases and other kinds of Data Since we hid the marker data earlier let S now take a look at this information Make sure the Hap1otypes Barcodes and Markers boxes are checked in the Display format dialog box The screen
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