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LymphGen genelist #3

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Tesson98 opened this issue Feb 2, 2023 · 0 comments
Open

LymphGen genelist #3

Tesson98 opened this issue Feb 2, 2023 · 0 comments

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@Tesson98
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Tesson98 commented Feb 2, 2023

Dear @ckrushton,
Thanks for creating this useful tool to generate inputfiles for LymphGen.
I classified my lymphoma patients with LymphGen and found your tool easy to use. However, I was wondering why we can just include ~130 genes in CNV results casue you noted "While the --lymphgen_genes file is optional, it is STRONGLY recommended when you are including CNVs, as I have noticed certain copy number features being dropped if too many CNVs are provided to LymphGen".
I didn't find the cnv genelist from papers(published in NEJM[1] and Cancer Cell[2]) or original code[3] from @wrightge and his group, so maybe I missed some informations. Could you share me the origin of those LymphGen genelist and give me some advices?
Really hope for your suggestions and wish you a good day!

Tesson,
2nd,2023

[1] Schmitz R, Wright GW, Huang DW, et al. Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma. N Engl J Med. 2018;378(15):1396-1407. doi:10.1056/NEJMoa1801445
[2] Wright GW, Huang DW, Phelan JD, et al. A Probabilistic Classification Tool for Genetic Subtypes of Diffuse Large B Cell Lymphoma with Therapeutic Implications. Cancer Cell. 2020;37(4):551-568.e14. doi:10.1016/j.ccell.2020.03.015
[3] https://zenodo.org/record/3700087#.Y9tdenZBw7c

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