1. chrGeneticist introduction for reviewer Jinlian Wang Jinlian.wang@mssm.edu 10/8/2014

2. https://wangj27.u.hpc.mssm.edu/wes/index.html 2. Click “Run” 1. Download

3. Download and “Run” Keep Click ‘Run’

4. Double click “chrgeneticst.msi” to install the tool_1 Click ‘Next’

5. Installation path selection_2 You can use the default directory and click”Next”

6. Installing…

7. Installation done_3 Installed successfully. Click “Close” After ‘Close’, please check your desktop

8. Double click the icon to run the tool Double click the icon

9. Sign in User name is Mount Sinai email e.g. jinlian.wang@mssm.edu Default password is 9999999 for everyone Pull down the menu and select Reviewer Click ‘Sign in’

10. Reviewer Panel Click and Start reviewing your assignments Your Reviewed Assignments Browse Exit Click this to change your password

11. Assignments interface New assignment Not completed assignment Click to start review If your assignment is not submitted, the status is ‘Modified’

12. Reviewer’s master table Save your assignment Export assignment to excel Go Home Click ‘Next’ to submit your assignment

13. What does the master table function ? Master table help you to diagnose each variants & make decision based on some evidence. Check the detailed position information and structure of the variants through UCSC Genome browser. Look at the latest publication for each variants Review the pathogenic information of each variants from HGMD, OMIM, GeneCard, ClinVar at both gene and variants levels Provide population frequency information for each variants from ESP6500, 1k genomes. Allow you to check the detailed information of each variants though embedded IGV browser. Comment with your expertise opinion on each variants. Auto save the assignments every five minutes Export your assignments in the format of excel. Master table help you to diagnose each variants & make decision based on some evidence. Check the detailed position information and structure of the variants through UCSC Genome browser. Look at the latest publication for each variants Review the pathogenic information of each variants from HGMD, OMIM, GeneCard, ClinVar at both gene and variants levels Provide population frequency information for each variants from ESP6500, 1k genomes. Allow you to check the detailed information of each variants though embedded IGV browser. Comment with your expertise opinion on each variants. Auto save the assignments every five minutes Export your assignments in the format of excel.

14. Raw column from Ingenuity Variant categories Click ‘Transcript ID’ to IGV Gene level Variant level Population frequency Functional impact Diagnosis Suggestion or comments Summary of comments Reviewer and Administrator Function area of the master table

15. Functions include: 1) sort : click small triangle in the header of each column 2) adjust the width of each column same as excel 3) freeze column: select the column you want to freeze, right click the header, and put your mouse within the popup window, 4) Hide column: same as 3), check the column you want to hide, 5) Comments: right click the cell you want to add comments, once the color is blue indicating the cell selected and you can make comments. Right click the cell to add comments Right click the header to Freeze/add /remove columns Auto save Mouse over each cell show the out sourced link Small icon indicates the comment made Click the header to sort each column

16. Using IGV After you click the link of “Transcript ID”, IGV and.bam file of proband will be loaded automatically. In the current version, only proband bam file is included. The IGV is running in the server side, so no worries about pre-installation of IGV, only thing is make sure you have installed jdk 7. If you have used IGV before, you don’t need to install jdk 7. If not, please download it from : https://wangj27.u.hpc.mssm.edu/wes/index.html

17. Steps of IGV

18. IGV launched

19. If asking for update, check ‘Skip this update’

20. Submission Conform your submission Click ‘Next’ to submit your assignment Export your assignment to excel

21. Exported excel file

22. Submitted successfully Submitted successfully, a email will automatically send to administrator

23. History browse Click to browse the history

24. Uninstall from “control panel” 1. Click 2. Click All Programs 3. Control Panel 4. Click “Uninstall a program”

25. Uninstall chrGenticist 5. Right click “chrGeneticist” 6. Click “Uninstall”

26. Comments and Feedback Please give me your comments and suggestion by email: jinlian.wang@mssm.edu Or call me 202 468 6495 (cell phone) Welcome to suggest a good name for this tool