Alamut Focus-User-Manual
Contents
1. e Click on New Project The Alamut Focus interface opens a blank project after naming it e Click on Open Project and select an existing project from the list e A short link to recent projects is also available from the menu Project Recent Alamut Focus 1 0 User Manual 14 10 July 2015 Command Description New Creates a project Starting a new project opens a new one in a tab Current projects are still open they are not closed Open Opens a project Opening another project does not close current project s Save Saves changes made to the current project selected tab Recent Opens a recent project Project is open in a new tab Manage Opens a windows for renaming or deleting saved project s Add Variant Annotation Datasets to a project Click on a project tab in which you want to add dataset s imported variant annotation file s Click on View tab and Add button opens a window to select one or multiple imported file s into the current project Note Only Alamut Batch variant annotation file format is currently supported by Alamut Focus Data in Alamut Focus Variant Table Imported and annotated information for the visible project is arranged in the Variants Table on the Alamut Focus interface If multiple datasets are selected annotated variants are consecutively aggregated per dataset in the main table The Variants Table lists the genes and related transcripts that overlap variants identified2. s initials on each Alamut Focus installation Floating licenses are managed by our server and don t require any specific installation We do not recommend installation on a central server so that users may have their own parameters Installation in a CITRIX environment or Windows Terminal Service is possible Alamut Focus 1 0 User Manual 11 10 July 2015 Input Requirements Alamut Focus imports annotated variants SNVs indels and duplications reported in the Alamut Batch file format Alamut Batch file format is a tab separated file of annotations 1 line per variant or multiple lines per variant if the annotation is performed on multiple transcripts A full description of annotations is available in the Alamut Batch documentation Note Fields from VCF files such as FILTER QUAL GT DP can be reported in the last output columns of Alamut Batch file format Please look at the Alamut Batch documentation for more details Alamut Focus Software Interface When the Alamut Focus software launches the interface opens with a Home page with information about software last improvements and on the upper panel a toolbar menu and shortcuts with main commands The Alamut Focus interface is an interactive view of annotated variants in a gene and genomic context for selected sample s Use the interface commands to import variant annotation files browse data apply filters manage and export data
3. Annotated File displayed but they are not imported in the Alamut Focus Database Alamut Focus 1 0 User Manual 13 10 July 2015 Import Variant Annotation Files into Alamut Focus Click on Variants Import annotated file from the menu and Add to browse and select a set of annotated variant files Selected files are automatically imported one by one and are managed as datasets in Alamut Focus Then they can be loaded for display or added to a project Open Variant Annotation Files in Alamut Focus Click on Variants Open imported file from the menu and Select the annotated variant files you want to display IMPORTANT They cannot be added to a project because they are not imported as a dataset in Alamut Focus Create Open and Manage Dataset An Alamut Focus dataset corresponds to a set of annotated variants e Importing variant annotation file s creates automatically dataset s At this step one dataset corresponds to one sample When you import a multi sample variant annotation file this one will be split in datasets one dataset one sample e Click on Open Dataset and select one or several dataset from the list for display Command Description Open Opens one or more datasets Select several datasets displays them in one tab Manage Opens a windows for renaming or deleting dataset s Create Open and Manage a Project The Project menu includes commands to create open save and manage projects
4. interactive biosoftware 1 4 foc ed User Manual Alamut Focus 1 0 User Manual 1 10 July 2015 Alamut Focus 1 0 User Manual This document and its contents are proprietary to Interactive Biosoftware They are intended solely for the contractual use of its customer in connection with the use of the product s described herein and for no other purpose This document and its contents shall not be used or distributed for any other purpose and or otherwise communicated disclosed or reproduced in anyway whatsoever without the prior written consent of Interactive Biosoftware Interactive Biosoftware does not convey any license under its patent trademark copyright or common law rights nor similar rights of any third parties by this document The instructions in this document must be strictly and explicitly followed by qualified and properly trained personnel in order to ensure the proper and safe use of the product s described herein All ofthe contents of this document must be fully read and understood prior to using such product s O 2015 Interactive Biosoftware All rights reserved Alamut Focus 1 0 User Manual 2 10 July 2015 Table of Contents Pd egene E AA A AAA 6 How To Use This Manual escindida AE 6 Purpose of This Manual nak nen akena ek Er R anek nn kU an week ek ae anln kr ka Bak den xan babek essa serais sas 6 AUN rU 6 Text CONVENTIONS ssa 6 User Attention Words
5. 3 Filter annotated variants based on any combination of filtering options Save filter for reuse in other projects 4 Classify variants according to their biological impact 5 Export data to text files Alamut Focus dataset or Alamut Visual mutation files System Requirements Installing the Alamut Focus software requires the following system specifications e 32 bit or 64 bit Windows OS Windows XP or later or MAC OS X Snow Leopard Lion Mountain Lion Mavericks Mac OS X 10 6 10 7 10 8 10 9 e Quad Core Processor 3 GHz minimum e 4GB RAM minimum e 200 MB hard drive space for installation e Internet connection required Note Linux is not currently supported Note An internet connection is required for license activation for searching variants and viewing genes Note Free disk space is also required to store projects and annotated variants For more details see Define an Alamut Focus database on page 29 Installation Alamut Focus must be installed in accordance with its license type floating license Alamut Focus 1 0 User Manual 9 10 July 2015 The floating license allows you to install Alamut Focus on an unlimited number of computers within the lab with a concurrent access to Alamut Focus restricted to a fixed number of users in accordance with your purchase order Note The number of concurrent users has been defined with our sales department when you purchased the Alamut Focus softwar
6. Application Variants Filter Project View and Help Data Tab shows data such as a project or a variant with related annotations Filter Panel provides options for filtering data using any combination of filters and displays a filter history showing all filters applied to the project Variants Table displays a table with imported variant annotations It is the main table of the Alamut Focus interface Gene Transcript View shows a graphical overview of the selected gene transcript Exons are displayed in blue introns in yellow and the variant is in red Note When resizing the Alamut Focus windows display is automatically resized Depending of data loaded in Alamut Focus it can take quite a bit of time to display data Import or Open Variant Annotation Files There are 2 ways for loading variant annotation files in Alamut Focus depending whether you want to integrate all annotated variants in the Alamut Focus database or simply display annotated variants in Alamut Focus The File menu includes commands to import or open variant annotation files IMPORTANT Only Alamut Batch annotated file format is currently supported by Alamut Focus Command Description Import Opens a window to browse a file location and import one or multiple Annotated File selected annotation file s All variants will be imported in the Alamut Focus Database Open Opens a window to select one annotation file into a tab Variants are
7. Selected Columns 16 Modity Column ge DEE 16 Modity N miber of Lies ra e test me 16 VCF Fields Reported in the Variants Table 16 Chapter 2 Applying Filters usessseeseeeseeeeeeee nennen enne enne nn KE KAKA KA KAREKE KA KA KA KAKE A KA KA KA KAKA KA KAR 18 AD DIV R LE A SS e ee EE De EE 18 General TE 18 EELER HU CET 19 Population Frequency Eltere 19 CONSEQUENCE Elton AI rt deve date lees bo 20 CUSTOM A e CD e DE 21 StudyiDesign H sussa tt Ete t ttem tt t hti tet es 22 Save Mariage and Reuse Filters ee cb tere e edt ees 25 Filter Settings ie in NT i ei 26 Disable Automatic Filtering sis morieris pebra aeaiia sena nnn nns n le da k kane b 9 tenga nis 26 Create a Keyboard Shortcut to Execute a Filter 26 Chapter 3 Managing Variants o all u lake k de Swed kena k ne Kul nennen nennen Hard e kaya ok xu W ya n ehe dan kul k nk Se kek n e kak 27 Quick Search Variante ax sael s ned EES AEN k s keye k t nh k k vik a a en Y dada ud Rho We ka d ev van LEES 27 Annotate Variants aw yay Lala nea eke ke a 28 Manage Variante EESTI ccc S 28 Save VNS 28 Export Elle EC 29 Export RER UE 29 Alamut Visual Mutation Files res cnn n nr non nannn can nn KEKE KAKA KAKA KAKA KRA KRA 29 AlamutiFocus DataSet egene AE 29 View a variant in Alamut Visual 4ima kar dan d ya kad alan ayak aka d k za da netten inset rese rns 29 Manage Vari
8. copy the program to your desired location where you have write permissions usually your Applications folder and run it Copying the program is performed simply by using drag and drop The first time you launch the software you have to enter your credentials Institution Id and License Key as they have been provided by our sales department when you purchased the software Inside the folder where you have uncompressed the downloaded file 1 Double click on the Alamut Focus program file Alamut Focus to launch it 2 Accept the End User License Agreement 3 Inthe Settings dialog box menu Application Settings Globals tab a Enter your Institution Id and License Key as they have been provided by Interactive Biosoftware b Enter User initials IMPORTANT If your internet access is behind a proxy enter the Proxy Settings this may require the input of an IT administrator 4 Inthe Settings dialog box menu Application gt Settings Network tab a Check the box Use a proxy server to configure the proxy settings b Complete the field with the help of your local IT staff 5 Alamut Focus is now ready to use You can either proceed to a standard installation on each computer or proceed to a standard installation on one computer and then copy it on the other computers so that all parameters such as institution id license key proxy will be the same In both cases we recommend to enter different user
9. BI Exome Sequencing Project alternative allele frequency and Minor Allele Frequency MAF from the following super populations are available African American AA European American EUR and all populations ALL e ExAC from the Exome Aggregation Consortium Alternative allele frequency from the following super populations are available Latino AMR South Asian SAS East Asian EAS African AFR European Non Finnish NFE European Finnish FIN Other populations OTH and all populations ALL Note This filter is available if variants have been annotated with Alamut Batch 1 4 Otherwise the filter is greyed out Consequence Filters Use the Consequence filters to filter data by variants that alter the coding potential of the transcript Options include coding effect clinical impact and in silico prediction filters Filter name Coding effect dbSNP Clinical Significance Clinical Impact HGMD Phenotype Clinical Impact Description Filters data to show any combination of Synonymous Missense Nonsense In frame Frameshift Start loss Stop loss None no coding effect Filters data to show any combination of Pathogenic Benign Other and unknown Pathogenic refers to pathogenic or likely pathogenic Benign refers to benign or likely benign Unknown refers to uncertain significance or unknown Not provided refers to not provided or untested Other refers to not Pathogenic and not Benign
10. Figure 1 Alamut Focus Interface Application File Dataset Fiter Project View Help Menu and Commands b la ba BS BS o Dome X fasc short gi n X Data tab General Gene Consegue Popdeton Freqercy StdvDemp Gett Ven Filter Panel D Irhertance Mode Dataset Qualification Affected V De Novo Study case 7 Y Autosonal Dominant Recesove dataset Lid pos annnotatedReasor gene gene 7 strand transten protein Unipeot gn v 112536264 ANAPCI 19988 NM 0226623 A 7688 ema GMa 112536 E 150719902 ATG98 neo momoi 4 sa 1073 v 42415020 ATPSAL us NM oos 1 am Ne maen oo 424150 E 4205020 55291 4 8189 NP 0010989991 24150 E 10530218 1032 NP 0010351214 eg 105302 n 11301753 1 wm NPAMSS2 era mm E 167453530 1813 NP 9198103 1653 7 167453530 um NE mee op 167453 E 151818777 mo re mmm oe 15 88 D 14906306 4003 eu ASPLI3 19161 nm 6302418 3765 NP 0011660451 ewou E 63018 2 son E ema 3140 QENEMO esou E 13046607 as 13046 n 130146607 zan 13014 7 130145607 zn 13048 v 130146607 2493 QSEBS2 130146 E 130146607 ua 13046 n 13046607 ET 13046 n 154456772 em vas 1556 n 158572476 xu wu 158872 Pagel ai Displaying 1 2 of21 49997 Variants Table amat Focus 1 0 0 2015 interactive Bemoftmare Alamut Focus 1 0 User Manual 12 10 July 2015 Menu and Commands includes commands for managing projects variant annotation files filters and variant quick searches Commands are organized in six sections
11. a variant in the Variants Table select Open in Alamut Visual to open an Alamut Visual variant windows Alamut Focus 1 0 User Manual 29 10 July 2015 Note Alamut Visual has to be running on the computer where Alamut Focus is used The Alamut Visual API feature has to be enabled Please look at Alamut Visual documentation Programmatic Access for more details Note Pathogenicity classes defined for variants in Alamut Focus are not displayed in Alamut Visual through this functionality Manage Variant Settings Define an Alamut Focus database Alamut Focus offers several ways to store variants and related annotations Type of Description database Local The local database named variant db and localized in the Alamut Focus installation directory Note It corresponds to the default database setting SQLite Browses directory paths to define another database location IMPORTANT The file extension must be db MySQL Defines a network connection to a MySQL RDBMS The following pieces of information are mandatory e The hostname where MySQL is installed e The name of the database The database has to be first created This database will be used to store Alamut Focus variants and related annotations e A MySQL user account with relevant privileges read and write rights to the previously defined database IMPORTANT Please contact your IT department for setting a MySQL database for Alamut Focu
12. able Automatic Filtering Filtering is done automatically by default after any filtering setting To change the default setting 1 Select Application Settings Filter and uncheck Automatically Apply Filter 2 Click on Apply to save and reopen Alamut Focus to enable the change Create a Keyboard Shortcut to Execute a Filter 1 Select Application gt Settings gt Filter click on the field Update filter key sequence and Press a key or keyboard combination to create a keyboard shortcut to execute a filter 2 Click on Apply to save and reopen Alamut Focus to enable the change Alamut Focus 1 0 User Manual 26 10 July 2015 Chapter 3 Managing Variants Alamut Focus allows you to apply annotations and classify variants according to their biological impact Annotations and classification are stored in a local database and are displayed in the Variant Tab The Variant Tab displays all relevant information about the selected variant e Information displays a genomic and gene related description shortcuts to relevant third party tools as Alamut Visual a license is required Ensembl gene OMIM e Pathogenicity allows you to classify your variant with either the 3 Classes or the 5 classes pathogenicity classification IMPORTANT Pathogenicity class is not automatically defined Note The 3 classes and 5 classes classification schemes are present by default in Alamut Focus For more details see C
13. and not Unknown and not provided Filters data to show any combination of HGMD phenotypes from imported annotated files This filter is available if variant files have been annotated with HGMD Professional Otherwise the filter is greyed out Alamut Focus 1 0 User Manual 20 10 July 2015 SIFT missense only In silico prediction MAPP missense only In silico prediction AGVGD missense only In silico prediction Splice Site In silico prediction Custom Filters A prediction of an effect of an amino acid substitution from Not scored to Deleterious on the function of a human protein based on SIFT This filter is available if variant files have been annotated with SIFT Otherwise the filter is greyed out A prediction of an effect of an amino acid substitution Good or Bad on the function of a human protein based on MAPP This filter is available if variant files have been annotated with MAPP Otherwise the filter is greyed out A prediction of an effect of an amino acid substitution from CO low to C65 high on the function of a human protein based on Align GVGD A prediction of the Splicing effect in variation vicinity done by Alamut Batch Filters data to show any combination of the following local splice effects New Donor Site New Acceptor Site Cryptic Donor Strongly Activated Cryptic Donor Weakly Activated Cryptic Acceptor Strongly Activated Cryptic Acceptor Weakly Activated Custom fi
14. ant Settings axika Wan n kak EE ENEE In xu A W n K k HED du WU H d kn ne dk vt US scene see z da kn ak 30 Alamut Focus 1 0 User Manual 4 10 July 2015 Define an Alamut Focus database ekere k keke keke kek keke KA KAKE KA KA KE A KAKA KI 30 Customize Pathogenicity Classification eene 31 Define Default Columns 2 lt i ts n de dede K a ceed kekan ert doe chek bereda a da deel de da du benek ak 31 Alamut Focus 1 0 User Manual 5 10 July 2015 Preface How To Use This Manual Purpose of This The Alamut Focus Software v 1 0 User Manual provides procedures Manual for using the software features Audience This manual is intended for laboratory personnel Interactive Biosoftware is not liable for damage or injury that results from use of this manual by unauthorized or untrained parties Text Conventions This manual uses the following conventions e Bold indicates user action For example Type 0 then press Enter for each of the remaining fields e Italic text indicates new or important words and is also used for emphasis For example Before analyzing always select gene e A right arrow gt separates successive commands you select from a drop down or shortcut menu For example Select File Explore Gene User Attention Two user attention words appear in Interactive Biosoftware user Words documentation Each word implies a particular level of observation or action as described below Note Prov
15. e Gene Filters data to exclude specified genes Exclude List To exclude genes click to open the gene list field next to the Exclude List options and enter the gene name This field is case sensitive Gene Filters data to show any combination of variant location in the gene Variant Location upstream 5 UTR exon intron 3 UTR downstream splice site Population Frequency Filters Use the Population Frequency filters to filter data based on the allele frequency in population studies Use the up down arrows to specify a value expressed as percentage select the right symbol for the comparison and then select the checkbox to apply the filter Options include global frequency from dbSNP and population frequencies from 1000 Genomes Project 1000 Genomes Exome Sequencing Project ESP and Exome Aggregation Consortium ExAC e dbSNP from NCBI Minor Allele Frequency MAF from 1000GP and the option Only RS validated are available For more information please look at the NCBI dbSNP e 1000 Genomes from 1000 Genomes Project Alternative allele frequency from the following super populations are available American AMR South Asian SAS East Asian EAS African AFR European EUR and all populations ALL Note 7his filter is available if variants have been annotated with Alamut Batch 1 3 and later Otherwise the filter is greyed out Alamut Focus 1 0 User Manual 19 10 July 2015 e ESP from the NHL
16. e To modify the number of concurrent users please contact our sales department sales interactive biosoftware com To install Alamut Focus you have to follow these basic steps standard installation 1 Download the file according to your computer operating system OS e Windows XP or later o Choose one of the following versions depending of your OS 32 bit versions 64 bit versions o Choose one of the following formats Zip file zip Self extractable executable exe e MACOSX Snow Leopard Lion Mountain Lion Mavericks Mac OS X 10 6 10 7 10 8 10 9 The program is available as a Disk image dmg Note For Mountain Lion OS X 10 8 and Mavericks OS X 10 9 users this external web page describes how to enable installation of applications from sources other than the Mac App Store 2 IMPORTANT a Zip file zip instruction Uncompressing has to be done into a folder where you have write permissions b Self extractable executable exe instruction Launch the executable file from anywhere and select a folder where you have write permissions to extract the content c Disk image file dmg instruction Alamut Focus 1 0 User Manual 10 10 July 2015 Insert or mount the disk image into the machine by double clicking the disk image file Having done this the disk image will appear as another device in the Finder An application bundle to install Alamut Focus is provided by us All you have to do is
17. ets to a project on page 14 2 Use the checkbox Affected if the phenotype is expressed Alamut Focus 1 0 User Manual 24 10 July 2015 3 Select the checkbox for the type of inheritance mode you want to be applied on your data Select a type from the following choices o De novo Filters variants not present in the family members o Autosomal Dominant Filters variants that are present in the affected family members and not present in the unaffected family members Note This filter requires that you indicate the affected family members o Autosomal Recessive Filters variants that are present in both unaffected parents as heterozygous variants and homozygous in the affected case o Autosomal Recessive Compound Heterozygosity Filters variants that are present in unaffected parents as different heterozygous variants and heterozygous in the affected case for the same gene Note This inheritance mode is not yet implemented o X linked Recessive Filter variants that are homozygous in affected females and heterozygous in both parent or variants that are hemizygous in affected males and not present in the father Note This filter requires that you indicate if the study case is a male or a female by using the drop down list o X linked Dominant Filter variants that are heterozygous in affected females and present as heterozygous in the affected parent or variants that are hemizygous in affected males and present as heterozy
18. gous in the affected mother Note This filter requires that you indicate the affected family members and if the study case is a male or a female by using the drop down list Note This inheritance mode is not yet implemented Save Manage and Reuse Filters To save any combination of filtering options for use with a different sample or for later use in another project save the filtering options The Filter menu includes commands to create open save apply and manage saved filters Alamut Focus 1 0 User Manual 25 10 July 2015 Command New Open Save Save as Recent Manage Description Creates a filter Starting a new filter opens a new one in a tab Current filters are still open they are not closed Opens a filter Opening another filter does not close current filter s Saves changes made to the currently open or applied filter selected tab Opens a dialog box for naming the filter Opens a recent filter Filter is open in a new tab Opens a windows for renaming or deleting saved filters Applying a saved Filter on a project consists in the following steps 1 Select Filter Apply from the toolbar menu 2 Select a filter name from the list The filter is applied automatically 3 To change to another saved filter select Filter Apply from the toolbar menu and select a different filter name Note The filter is applied on the current project not on all open projects Filter Settings Dis
19. ides information that may be of interest or help but is not critical to the use of the product IMPORTANT Provides information that is necessary for proper operation use or best practices for the Alamut Focus Software How To Get More Information Related e The Alamut Focus Software features help is accessible by Documentation selecting Help Documentation from the toolbar Alamut Focus 1 0 User Manual 6 10 July 2015 Contacting Interactive Biosoftware How To Get To get support for Alamut Focus only select Help Contact This Services and opens your default messaging tool such as MS Outlook or Support Thunderbird to send an email to the Interactive Biosoftware Technical Support team support interactive biosoftware com For any issues see the Troubleshooting Checklist on page 7 before contacting Technical Support For any other requests the latest services and support information for all locations go to http www interactive biosoftware com then click the link for CONTACT On the Contact page you can Submit a question directly to Technical Support by selecting the appropriate subject in the drop down list In addition the Contact page provides access to telephone and fax numbers to contact Interactive Biosoftware Troubleshooting Please complete the checklist before contacting Technical Support Checklist Table 1 Troubleshooting Checklist Y Information for Technical Support Briefly summarize the pr
20. in the dataset Each row of the table contains the gene and reported variant Genes that include multiple variants are listed multiple times in the table once for each variant Note If you performed annotation with all transcripts in Alamut Batch genes that include multiple transcripts are listed multiple times in the table once for each variant Note Currently annotated information corresponds to the variant annotation file format generated by Alamut Batch with default parameters For more details see the Alamut Batch documentation Alamut Focus 1 0 User Manual 15 10 July 2015 Annotation Fields Reported in the Variant Table To modify how data appear in the table click on the column heading to sort data in descending or ascending order Note Modifying how data appear in the Variants Table only affects the way information is arranged in the table Modifying views does not change the underlying data Sort Data in Ascending or Descending Order To change the order in which data appear in the Variants Table click on a column heading Data are sorted in either descending or ascending order of values listed in that column Click again to reverse the order Note Sorting data is done only on one column Sorting cannot be done on several columns at the same time Show or Hide Selected Columns Select View tab and use the checkboxes to show or hide specific columns in the Variants Table Select the checkbox to sh
21. in which candidate disease causing variants are researched will be identified Note Only one case can be defined per study Father Mother Labels used to describe a family based study Sister or Brother Control Label used to describe control sample s in a study Note This label is not yet implemented Affected A phenotype related to the study is expressed 2 The Inheritance Mode allows you to define the manner in which a particular genetic trait or disorder is passed from one generation to the next Inheritance modes available in Alamut Focus are described below Inheritance Mode Description Alamut Focus 1 0 User Manual 22 10 July 2015 De novo Autosomal Dominant Autosomal Recessive Autosomal Recessive Compound Heterozygousity X linked Recessive An alteration in a gene that is present for the first time in one family member as a result of a mutation in a germ cell egg or sperm of one of the parents or in the fertilized egg itself from GeneReviews Causative variants are not present in the relatives and are either homozygous or heterozygous in the affected case Describes a trait or disorder in which the phenotype is expressed in those who have inherited only one copy of a particular gene mutation heterozygotes specifically refers to a gene on one of the 22 pairs of autosomes non sex chromosomes from GeneReviews Causative variants are present in an affected parent as heterozygous variants a
22. lect Edit Variant to open a Variant Tab Note You can also directly double click on the desired variant from the Variant Table 2 Use the Classification drop down lists to choose the preferred Pathogenicity Classification 3 Use the Class drop down lists to choose the desired Pathogenicity Class for your variant 4 Use the Comments text area to give additional information concerning the variant 5 Click on Save to store annotations Note Pathogenicity class is not automatically defined We suggest that you use the most recent Practice Guidelines for the Evaluation of Pathogenicity and Reporting of Sequence Variants in Clinical Molecular Genetics from the UK Association for Clinical Genetic Science and the Dutch Society of Clinical Genetic Laboratory Specialists to classify variants Note The default classification scheme can be set through the menu Application Settings Classification Pathogenicity classes and colors can be customized For more details see Customize Pathogenicity Classification on page 30 Note All modifications made to the variant classification are stored Manage Variants Save Variants Variants that are imported and then managed by dataset are automatically stored into an Alamut Focus database Alamut Focus 1 0 User Manual 28 10 July 2015 Saved user defined annotations and classification related to variants are stored into the Alamut Focus database History informati
23. lters enable filtering based on columns provided in the imported variant annotation files 1 Select a column from the list 2 Choose the right operator Note The operator In checks for the presence of the string inside a list of values with a comma separator between them For instance a list of digits 1 2 and 3 will be entered in the field Value like this 1 2 3 without quotes 3 Enter a value or select another field name for a selected field 4 Click Add to create a custom filtering Alamut Focus 1 0 User Manual 21 10 July 2015 5 Use any combination of fields from any number of fields Filters are applied to the current table tab therefore to all samples that are imported into the project 6 Select a filter condition and click Delete to remove the related applied filter Click Delete All to remove all applied custom filters IMPORTANT The Custom Filter search engine is case sensitive Study Design Filters Use the Study Design filters to filter variants that are consistent with an inheritance mode and provided variant data for available family members or case and control samples This filter is useful in identifying candidate disease causing variants The filter is composed of two parts 1 The Description allows you to describe qualification affected or unaffected selected datasets in the study context Qualification name Description Study Case The case that is studied and
24. nd are heterozygous in the affected case Describes a trait or disorder requiring the presence of two copies of a gene mutation at a particular locus in order to express observable phenotype specifically refers to genes on one of the 22 pairs of autosomes non sex chromosomes from GeneReviews Causative variants are present in both unaffected parents as heterozygous variants and are homozygous in the affected case An individual who has two different abnormal alleles at a particular locus one on each chromosome of a pair usually refers to individuals affected with an autosomal recessive disorder from GeneReviews Causative variants are present in unaffected parents as different heterozygous variants and are heterozygous in the affected case for the same gene Note This inheritance mode is not yet implemented A mode of inheritance in which a mutation in a gene on the X chromosome causes the phenotype to be expressed in males who are hemizygous for the gene mutation i e they have only one X chromosome and in females who are homozygous for the gene mutation i e they have a copy of the gene mutation on each of their two X chromosomes Carrier females who have only one copy of the mutation do not usually express the phenotype although differences Alamut Focus 1 0 User Manual 23 10 July 2015 in X chromosome inactivation can lead to varying degrees of clinical expression in carrier females from GeneReviews Causative variant
25. oblem Have you been able to repeat the problem If yes list the steps that you perform 1 2 3 Indicate the configuration of your Alamut Focus Software Software License Type Software License Key Software Version Alamut Server Have you set a Proxy Server Summarize your computer s specifications Operating System OS OS Version Have you upgraded the OS service packs OS versions etc If yes which ones Alamut Focus 1 0 User Manual 7 10 July 2015 Send Us Your Interactive Biosoftware welcomes your comments and suggestions for comments improving user s documents You can e mail your comments to contact interactive biosoftware com If you published biological results and you used Alamut Focus as a part of your analysis approach please cite us as following Alamut Focus version 1 0 Interactive Biosoftware Rouen France www interactive biosoftware com How To Cite Us Alamut Focus 1 0 User Manual 8 10 July 2015 Chapter 1 Getting Started Introduction The Alamut Focus software imports annotated variants from Alamut Batch files After import Alamut Focus provides commands to filter variants using filtering options manage and export data A basic Alamut Focus workflow consists in the following steps 1 Create a project or open an existing one 2 Import variant annotations in Alamut Batch file format Import one sample or multiple samples into a project
26. on also stored are the date when the variant is saved the classification and pathogenicity class comments made by a user and the user itself initial Note The default setting for the Alamut Focus database can be modified For more details see Define an Alamut Focus database on page 29 Export Variants Alamut Focus provides features for exporting variants to text files or for displaying the variant in Alamut Visual Export Data Files Exporting filtered variants and their annotations generates a tabulated separated values Tabulated or a comma separated values CSV file These text file format are not application specific and can be opened in any text editor Note Exported columns are those that are displayed in the Variant Table Alamut Visual Mutation Files IMPORTANT Please do not export directly in your Alamut Visual Mutation Directory by default it corresponds to AlamutFiles otherwise your Alamut Visual mutation files will be overwritten Exporting filtered variants with this option generates Alamut Visual Mutation files one file one gene Then you can import variants into Alamut Visual gene per gene Alamut Focus Dataset Exporting filtered variants with this option creates an Alamut Focus Dataset To open the exported dataset go to the menu Dataset Open View a variant in Alamut Visual Viewing a variant from Alamut Focus to Alamut Visual is very simple Right click on
27. ow data and clear the checkbox to hide data All columns are set to show by default Modify Column Order Select a column with the mouse left button and move the selected column to another location Modify Number of Lines Click the checkbox Number of Lines at the bottom of the table and select the number of displayed lines per page Note Currently the table layout is saved for a project and cannot be used for other projects VCF Fields Reported in the Variants Table Alamut Batch allows you to import columns from VCF files in its annotated variant files Several fields from VCF files can be populated through Alamut Batch and are then accessible in the Variants Table of Alamut Focus The column heading will be named by the field name or the ID used in the VCF file Alamut Focus 1 0 User Manual 16 10 July 2015 IMPORTANT Please refer to the documentation of Alamut Batch and the VCF header of the VCF file to use the right parameters to populate columns from VCF files Alamut Focus 1 0 User Manual 17 10 July 2015 Chapter 2 Applying Filters Apply filters The Filters panel provides options for applying any combination of filters to the data in your project Filters are grouped in sections General Study Design Gene Population Frequency Consequence and Custom The Filter Summary at the right hand side of the Filter panel displays all filters applied on your project and the number of unfiltered variant
28. ren entren eL Eve Eb epe ida 6 How To Get More Information 6 Related Documentation teri ide iaa 6 Contacting Interactive Biosoftware keke kk kK nene KAKA KAKA KA KA KA KA KAKA A KA KA KA KAKA 7 How To Get Services and KT ee E 7 Troubleshooting Checklist tien rre eme a puc reee ks e n k Pee Des dees 7 Send s folsIgiee ei iD Tocem 8 How To Cite US C 8 Chapter 1 Getting Started E 9 IR E rO dU G lO ET 9 en Hun CN 9 hcl io amei dadas 9 Input RequiteMentS hence nad ene eR RE 12 Alamut Focus Software Interface 12 Import or Open Variant Annotation Files kak kek kk kK KAKA KA KAKA K KAKA AA 13 Import Variant Annotation Files into Alamut Focus 14 Open Variant Annotation Files in Alamut9 FOCUS c cccccsccccecssecesecsseceeseseeeeceeaeeeeeeaeeeseesseeeeeees 14 Create Open and Manage Dataset ssssssssssssseseseeeeen k na dala ask de k zu kla asas essi ntis de nian da da 14 Create Open and Manage a Project 14 Add Variant Annotation Datasets to a porolert nennen nnne KAKA KAKA KAKA KA KA KA KA 15 Data ir Alamut Focus Variant Table teer eter ttn lan ki dakn ala kann klanan Sena k ka kan nan 15 Annotation Fields Reported in the Variant Table 16 Alamut Focus 1 0 User Manual 3 10 July 2015 Sort Data in Ascending or Descending Order 16 Show or Hide
29. riant Table To do that 1 Select Application Settings Filter click on Select on the right hand Default columns text 2 Select columns and click on Apply from the Select columns window to save 3 Click on Apply again from the Setting window to save Alamut Focus 1 0 User Manual 31 10 July 2015
30. s 1 Click on a tab to expand a filter section 2 From the available options selecting filter settings applies automatically filters 3 Use any combination of settings from any number of filters 4 Unclick on filter settings to remove related applied filters Filters are applied to the current table tab therefore to all samples that are imported into the project You can create a filter using any combination of the filter options in the Filters panel and then save the combination as a single filter Note Saved filters can later be applied to other projects For more information see Save Manage and Reuse Filters on page 24 General Filters Use the General filters to filter data by Variant Type Genotype and Chromosome Filter name Description Variant Type Filters data to show any combination of Substitutions Insertions Deletions or Duplications Genotype Filters data to show any combination of heterozygote or homozygote Chromosome Filters data to show all chromosomes default autosomal chromosomes or a specific chromosome Alamut Focus 1 0 User Manual 18 10 July 2015 Gene Filters Use the Gene filters to filter data by location and or include or exclude specific genes Filter name Description Gene Filters data to include specified genes Include List To include genes click to open the gene list field next to the Include List options and enter the gene name This field is case sensitiv
31. s Memory Stores temporarily variants and related annotations in the Random Access Memory RAM where Alamut Focus is installed Memory storage is faster but has a limited capacity relative to the available RAM Alamut Focus 1 0 User Manual 30 10 July 2015 Note Currently 1MB is required for 1 000 variants and related annotations By default the Alamut Focus database is saved locally in the Alamut Focus installation directory The database corresponds to a file named variant db When the database is stored locally or in memory variants and related annotations are available for projects opened on that computer If the database is stored on a network location SQLite or MySQL annotations are available to projects opened in any installation of Alamut Focus with access to that network location 1 To change the default setting select Application Settings Database and Use the Connection Type drop down lists to choose a type of database connection 2 Complete all the fields 3 Click on Apply to save and reopen Alamut Focus to enable the change Customize Pathogenicity Classification The default pathogenicity classification scheme can be set through the menu Application gt Settings Classification by selecting either a 3 classe or 5 classe scheme Pathogenicity class labels and colors are customizable Define Default Columns You can define the default columns that will be displayed in the Va
32. s are present in affected males sons as hemizygous and not present in the father or present in affected females daughters as homozygous exceptionally rare in X linked recessive disorders Note Males affected with an X linked disorder cannot transmit it to their sons X linked Dominant Describes a dominant trait or disorder caused by a mutation in a gene on the X chromosome The phenotype is expressed in heterozygous females as well as in hemizygous males having only one X chromosome affected males tend to have a more severe phenotype than affected females from GeneReviews Causative variants are present in the affected mother and daughters as heterozygous variants and affected sons as hemizygous variants or present in the affected father and daughters as heterozygous variants Note Males affected with an X linked disorder cannot transmit it to their sons Note This inheritance mode is not yet implemented IMPORTANT Define a study case is mandatory for the Study Design Filter In the Description section all selected datasets are listed to be used in the inheritance mode analysis 1 Use the Qualification drop down lists to annotate your dataset Select at least one case study case and parent mother father sibling sister brother or control if necessary Note All samples to be used in the Study Design filtering must be present in the current project For more information see Add Variant Annotation Datas
33. ustomize Pathogenicity Classification on page 30 e Same variants displays imported variant annotation files in which the variant is also present found e Variant data displays a short overview of the variant annotations in the current project e Variant history displays all modifications made to the variant classification e Comment is a free text field Quick Search Variants Go To implements a quick search feature that allows convenient access to variants through all imported variant annotations in Alamut Focus The different available queries are listed below e Access to Standard Genetic References HUGO approved gene symbols e Access to genomic positions The query format is lt chromosome gt lt start position gt lt end position gt ex X 73014142 73014142 1 Type a gene name for instance into the Go To to get variants related to the query 2 Select the right suggested query done by Alamut Focus This suggestion is only done for a gene or dataset query Alamut Focus 1 0 User Manual 27 10 July 2015 3 Clickon E to launch the search Note Accessing cDNA and protein positions is not yet implemented Note Accessing genomic and cDNA variants is not yet implemented Annotate Variants This functionality is only available for variants imported in Alamut Focus See Import Variant Annotation Files into Alamut Focus on page 13 1 Right click on a variant in the Variants Table se
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