How to extract phenotype from UKBiobank data?
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5.0 years ago
anamaria ▴ 220

Hello,

I am trying to create my phenotype file in order to perform GWAS.

I want my cases and controls to satisfy the definitions bellow and I plant to use this software: https://github.com/saphir746/BiobankRead-Bash/blob/master/README.rst

Case: 1.Eyesight questionnaire data field 6148 Diabetes related eye disease (case) (4,235) 2.Data-Field 41270 Diagnoses: - ICD10, Chapter IV Endocrine, nutritional and metabolic diseases: E10.3 (T1D with ophthalmic manifestations), E11.3 (T2D with ophthalmic manifestations), E14.3. Chapter VII Diseases of the eye and adnexa: H36.0 (diabetic retinopathy). Add together 1 and 2 to use as cases and remove duplicates.

Control: 1.Data-Field 2443 Diabetes diagnosed by doctor (control) Yes (29,572) 2.Data-Field 41270 Diagnoses:Chapter IV Endocrine, nutritional and metabolic diseases:E10.9, E11.9, E14.9 (diabetes without complications).Add together 1 and 2 to use as controls and remove duplicates.

They have this example listed on the github page:

python extract_HES.py .... --codes ICD10LC.txt (ICD10LC.txt contains C34, C340, C341, C342, C343, C348, C349) --codeType ICD10 ....
python extract_HES.py .... --codes ICD9LC.txt (ICD9LC.txt contains 1620, 1622, 1623, 1624, 1625, 1628, 1629) --codeType ICD9 ....
python extract_SR.py .... --disease SRLC.txt (ICD9LC.txt contains 1001, 1027, 1028) --SRcancer True ...
python extract_death.py .... --codes ICD10.txt --primary True --secondary True ....

Do you know how what these .txt files would contain in my case? And do I need HES files for my example?

I am completely new to this, so please forgive my basic questions.

Cheers, Ana

ukbiobnk • 1.4k views
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