Open ivadym opened 6 months ago
Any updates on this?
@zahrahaider, I could look into this. There is a new CNV calling method bioinformatics tool called Jumble. In the mean time, it will be helpful if you could provide us with some specific region(s) along with the case(s) where you identify needs improvement and we can look at it more closely and fix and/or improve the method.
Hi Khurram, The cases I am working on right now pertain to this ticket #910093 where we ordered tumor-only analysis of cfDNA samples using a panel of normals (built on gDNA) for the GMS lymphoid panel 7.3. I used the cns segment data from balsamic cnvkit output and ran it through GISTIC where we repeatedly saw artefacts in chr19 and chr20, and amplifications in 8p24 in almost 75% of patients which shouldn't be there. I am posting the gistic plots of Amps/Dels that we see most frequently in our cohort. I would like some help in also deciding parameters for running gistic.
Refinement meeting comments:
To resolve the issue we looked at the CNV analysis and identified the following:
We proposed the following immediate solution:
Case | All segments from .cns | CNV segments from *..svdb.clinical.filtered.pass.vcf.gz |
---|---|---|
1 | 70 | 27 |
2 | 67 | 65 |
3 | 75 | 27 |
4 | 60 | 58 |
5 | 55 | 54 |
6 | 66 | 13 |
7 | 63 | 21 |
8 | 71 | 69 |
9 | 53 | 53 |
10 | 63 | 60 |
11 | 59 | 15 |
12 | 70 | 68 |
13 | 55 | 55 |
14 | 66 | 63 |
15 | 60 | 59 |
16 | 79 | 24 |
17 | 59 | 57 |
18 | 72 | 70 |
19 | 59 | 58 |
20 | 76 | 45 |
21 | 66 | 65 |
22 | 59 | 59 |
23 | 62 | 9 |
24 | 59 | 14 |
25 | 61 | 60 |
26 | 75 | 73 |
27 | 106 | 74 |
28 | 61 | 10 |
29 | 61 | 61 |
30 | 80 | 26 |
31 | 59 | 58 |
32 | 82 | 79 |
33 | 79 | 75 |
34 | 62 | 61 |
I hope this solved the issue with artefacts mentioned above.
Need
As a clinical geneticist, I need an improved CNV workflow for targeted panel sequencing (UMI & non-UMI), in particular for cfDNA samples, to accurately detect genetic variations.
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