Clinical-Genomics / BALSAMIC

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
https://balsamic.readthedocs.io/
MIT License
45 stars 16 forks source link

[User Story] Improve CNV calling for target workflow #1435

Open ivadym opened 5 months ago

ivadym commented 5 months ago

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.

Suggested approach

Considered alternatives

Deviation

No response

System requirements assessed

Requirements affected by this story

No response

Risk assessment needed

Risk assessment

No response

SOUPs

No response

Can be closed when

Blockers

No response

Anything else?

No response

zahrahaider commented 1 month ago

Any updates on this?

khurrammaqbool commented 1 month ago

@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.

zahrahaider commented 1 month ago

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.

amp_qplot.pdf del_qplot.pdf

mathiasbio commented 1 month ago

Refinement meeting comments:

khurrammaqbool commented 1 month ago

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.