Recoding who_diagnosis

[fpbarthel]

Recoded WHO diagnosis using following parameters:

UPDATE clinical.surgeries SET who_classification = NULL;

UPDATE clinical.surgeries SET who_classification = 'Diffuse Astrocytoma, IDH-mutant' WHERE histology = 'Astrocytoma' AND grade = 'II' AND idh_status = 'IDHmut';
UPDATE clinical.surgeries SET who_classification = 'Diffuse Astrocytoma, IDH-wildtype' WHERE histology = 'Astrocytoma' AND grade = 'II' AND idh_status = 'IDHwt';

UPDATE clinical.surgeries SET who_classification = 'Anaplastic Astrocytoma, IDH-mutant' WHERE histology = 'Astrocytoma' AND grade = 'III' AND idh_status = 'IDHmut';
UPDATE clinical.surgeries SET who_classification = 'Anaplastic Astrocytoma, IDH-wildtype' WHERE histology = 'Astrocytoma' AND grade = 'III' AND idh_status = 'IDHwt';

UPDATE clinical.surgeries SET who_classification = 'Glioblastoma, IDH-wildtype' WHERE histology = 'Glioblastoma' AND grade = 'IV' AND idh_status = 'IDHwt';
UPDATE clinical.surgeries SET who_classification = 'Glioblastoma, IDH-mutant' WHERE histology = 'Glioblastoma' AND grade = 'IV' AND idh_status = 'IDHmut';

UPDATE clinical.surgeries SET who_classification = 'Oligodendroglioma, IDH-mutant and 1p/19q-codeleted' WHERE histology = 'Oligodendroglioma' AND grade = 'II' AND idh_status = 'IDHmut' AND codel_status = 'codel';
UPDATE clinical.surgeries SET who_classification = 'Anaplastic Oligodendroglioma, IDH-mutant and 1p/19q-codeleted' WHERE histology = 'Oligodendroglioma' AND grade = 'III' AND idh_status = 'IDHmut' AND codel_status = 'codel';

UPDATE clinical.surgeries SET who_classification = 'Oligodendroglioma, IDH-mutant and 1p/19q-codeleted' WHERE histology IS NOT NULL AND grade = 'II' AND idh_status = 'IDHmut' AND codel_status = 'codel';
UPDATE clinical.surgeries SET who_classification = 'Anaplastic Oligodendroglioma, IDH-mutant and 1p/19q-codeleted' WHERE histology IS NOT NULL AND (grade = 'III' OR grade = 'IV') AND idh_status = 'IDHmut' AND codel_status = 'codel';

UPDATE clinical.surgeries SET who_classification = 'Diffuse Astrocytoma, IDH-mutant' WHERE histology = 'Oligoastrocytoma' AND grade = 'II' AND idh_status = 'IDHmut' AND codel_status = 'noncodel';
UPDATE clinical.surgeries SET who_classification = 'Diffuse Astrocytoma, IDH-wildtype' WHERE histology = 'Oligoastrocytoma' AND grade = 'II' AND idh_status = 'IDHwt' AND codel_status = 'noncodel';

UPDATE clinical.surgeries SET who_classification = 'Anaplastic Astrocytoma, IDH-mutant' WHERE histology = 'Oligoastrocytoma' AND grade = 'III' AND idh_status = 'IDHmut' AND codel_status = 'noncodel';
UPDATE clinical.surgeries SET who_classification = 'Anaplastic Astrocytoma, IDH-wildtype' WHERE histology = 'Oligoastrocytoma' AND grade = 'III' AND idh_status = 'IDHwt' AND codel_status = 'noncodel';

UPDATE clinical.surgeries SET who_classification = 'Diffuse Astrocytoma, IDH-mutant' WHERE histology = 'Oligodendroglioma' AND grade = 'II' AND idh_status = 'IDHmut' AND codel_status = 'noncodel';
UPDATE clinical.surgeries SET who_classification = 'Diffuse Astrocytoma, IDH-wildtype' WHERE histology = 'Oligodendroglioma' AND grade = 'II' AND idh_status = 'IDHwt' AND codel_status = 'noncodel';

UPDATE clinical.surgeries SET who_classification = 'Anaplastic Astrocytoma, IDH-mutant' WHERE histology = 'Oligodendroglioma' AND grade = 'III' AND idh_status = 'IDHmut' AND codel_status = 'noncodel';
UPDATE clinical.surgeries SET who_classification = 'Anaplastic Astrocytoma, IDH-wildtype' WHERE histology = 'Oligodendroglioma' AND grade = 'III' AND idh_status = 'IDHwt' AND codel_status = 'noncodel';

UPDATE clinical.surgeries SET who_classification = 'Diffuse Astrocytoma, NOS' WHERE histology = 'Astrocytoma' AND grade = 'II' AND idh_status IS NULL AND codel_status IS NULL;
UPDATE clinical.surgeries SET who_classification = 'Anaplastic Astrocytoma, NOS' WHERE histology = 'Astrocytoma' AND grade = 'III' AND idh_status IS NULL AND codel_status IS NULL;

UPDATE clinical.surgeries SET who_classification = 'Oligodendroglioma, NOS' WHERE histology = 'Oligodendroglioma' AND grade = 'II' AND idh_status IS NULL AND codel_status IS NULL;
UPDATE clinical.surgeries SET who_classification = 'Anaplastic Oligodendroglioma, NOS' WHERE histology = 'Oligodendroglioma' AND (grade = 'III' OR grade = 'IV') AND idh_status IS NULL AND codel_status IS NULL;

UPDATE clinical.surgeries SET who_classification = 'Glioblastoma, NOS' WHERE histology = 'Glioblastoma' AND grade = 'IV' AND idh_status IS NULL AND codel_status IS NULL;

UPDATE clinical.surgeries SET who_classification = 'Oligoastrocytoma, NOS' WHERE histology = 'Oligoastrocytoma' AND grade = 'II' AND idh_status IS NULL AND codel_status IS NULL;
UPDATE clinical.surgeries SET who_classification = 'Anaplastic Oligoastrocytoma, NOS' WHERE histology = 'Oligoastrocytoma' AND grade = 'III' AND idh_status IS NULL AND codel_status IS NULL;

[Kcjohnson]

I've updated the latest UCSF clinical data (received 2018.11.16) in the database.

There is one sample that progressed from grade II Oligoastrocytoma to a grade IV Oligoastrocytoma (GLSS-SF-0157-R1). I haven't updated the who_classification for this sample, but I suspect it should be classified as "Glioblastoma, IDH-mutant"?

[Kcjohnson]

Closing this because it has since been updated in the clinical.surgeries table as "Glioblastoma, IDH-mutant".