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Exome sequencing questionnaire
A joint ACGS/UKGTN meeting will be held on the 29th July to discuss how clinical exome and whole
exome sequencing, including the use of bespoke virtual subpanel testing, is being applied within
diagnostic testing. One outcome of the meeting will be to discuss the need for additional ACGS Best
Practice guidelines, particularly to cover bespoke testing. The second outcome is to establish a
protocol to list laboratories on the UKGTN web site so they can be recognised as carrying out
bespoke CES/WES. This is currently out of scope of the Gene test evaluation process. In order to
inform discussions we would like you to complete this questionnaire. Even if this is not something
you currently perform could you indicate this in the first question and then answer the last question
re attendance at the meeting.
1. Do you currently perform or plan to introduce either clinical exome or whole exome
sequencing (please specify which)?
___________________________________________________________________________
2. If you do which of the following applications do you use: (please tick all that apply):
a) Analysis of a specific sub panel of genes associated with specific condition(s) only
b) A bespoke gene panel designed specifically for the patient’s phenotype
c) Analysis of the entire exome or clinical exome
d) Other (please specify):
________________________________________________________________________
3. If you answered yes to 2b how do you select the gene panel and who is normally involved in
the discussion?
___________________________________________________________________________
___________________________________________________________________________
4. Which testing strategy is employed:
a. Testing of the index case only
b.
Trio analysis
c. Both depending on scenario (please specify with examples if possible)
5. Please describe how patients are selected for analysis if you answered yes to 2b, c or d. e.g.
at an MDT between lab and clinical geneticist
___________________________________________________________________________
___________________________________________________________________________
__________________________________________________________________________
6. Which capture kits (off the shelf/custom) are utilised for:
a) Clinical exome sequencing __________________________________________________
b) Whole exome sequencing ___________________________________________________
7. Which sequencing platform(s) do you use? ________________________________________
8. What internal quality control is used for exomes?
___________________________________________________________________________
___________________________________________________________________________
9. What validation is performed prior to offering bespoke subpanels?
___________________________________________________________________________
___________________________________________________________________________
10. What is your strategy for gap filling?
___________________________________________________________________________
___________________________________________________________________________
11. How is sequence alignment and variant calling performed? (commercial software/in-house
implementation)
___________________________________________________________________________
___________________________________________________________________________
12. How are variants annotated? (commercial software/in-house implementation)
___________________________________________________________________________
___________________________________________________________________________
13. How are variants prioritised? (are bioinformatics tools used)
___________________________________________________________________________
___________________________________________________________________________
14. How are variants interpreted? (are ACGS and/or ACMG guidelines used?)
___________________________________________________________________________
___________________________________________________________________________
15. How is coverage calculated? (eg after removal of reads failing QC, horizontal coverage at 20X
is calculated for each gene (a “gene” is defined as all refseq coding bases for that gene, plus
5bp into each non-coding region), and expressed as a percentage)
___________________________________________________________________________
___________________________________________________________________________
16. How do you report the level of analysis you have carried out such as coverage and gaps?
___________________________________________________________________________
___________________________________________________________________________
17. Do you report copy number changes or perform an alternative test where applicable?
___________________________________________________________________________
18. What is your strategy for Sanger confirmation testing?
___________________________________________________________________________
19. What is your strategy for reporting variants? (what is reported, are class 3’s reported, are
family members tested prior to reporting etc)
___________________________________________________________________________
___________________________________________________________________________
20. Do you discuss results in an MDT format and if so how has this been assembled? If not
please describe how variants for reporting are prioritised.
___________________________________________________________________________
___________________________________________________________________________
21. If applicable how do you report a variant which has not previously been associated with the
patients phenotype?
___________________________________________________________________________
___________________________________________________________________________
22. In scenarios 2b, c and d how many reports have you issued to date? ____________________
23. What is your reporting time for this test? _________________________________________
24. Do we need to create a new GenU band for this test? ________________________________
25. Please would you list the top 5 areas that should be covered in best practice guidelines:
a.
b.
c.
d.
26. Any other comments
___________________________________________________________________________
___________________________________________________________________________
27. Would you like to send a representative to the meeting?
Name:
Laboratory:
With many thanks
Yvonne Wallis, Joo Wook Ahn, Fiona Macdonald
Please return the questionnaire to [email protected].