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Repository for discussion of OpenSAFELY codelists
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*DISEASE*: splenectomy or sickle cell #4

Open sebbacon opened 4 years ago

sebbacon commented 4 years ago

Code for identifying binary variable for "splenetctomy or sickle cell"

CarolineMorton commented 4 years ago

LSHTM defintion:

Any history of asplenia or dysfunction of spleen including sickle cell disease

Need to decide re to include thalassemias

Need codelist from Grint paper. Emailed Helen M re this

CarolineMorton commented 4 years ago

~~LSHTM code lists aplastic_anaemia_updated_Jul18.xlsx other_cmi_immuno_updated_Jul18.xlsx~~ moved to ebmdatalab/tpp-sql-notebook#36

hmcd commented 4 years ago

Think the wrong codelists made it on here! Rather than aplastic anaemia and other_cmi_immuno this codelist should be spleen_Jul19.xlsx This codelist includes asplenia and dysplenia, including sickle cell disease. It doesn't include thalassaemias - could consider adding these.

hmcd commented 4 years ago

(Have codes for thalassaemias - clinical decision as to whether they should be included in this group?)

alexwalkerepi commented 4 years ago

DRAFT

DEFINITION: 2 columns for each of the codelists below: 1) a binary variable denoting the presence of one of the codes at any point in the patient record. 2) the earliest date of such a code.

POTENTIAL BIASES:

CLINICAL SIGN OFF & DATE:

EPIDEMIOLOGY SIGN OFF & DATE:

SHARED WITH WIDER TEAM: Yes/No

FINAL SIGN OFF DATE (and apply label)

hmcd commented 4 years ago

(1) Dysplenia and (2) Sickle Cell Disease (separate exposures)

DEFINITION: (1) Patients with asplenia or dysplenia ever recorded. (2) Patients with a diagnosis of sickle cell disease ever recorded.

Output 3 columns for each of dysplenia and sickle cell disease : 1) a binary variable denoting the presence of one of the codes at any point in the patient record (2) a string variable with the Read term for the earliest recorded code (3) the earliest date of this code

example patient_id spleen_bin spleen_term spleen_date sickle_bin sickle_term sickle_date 123 1 Total splenectomy 1/2/2009 1 Asplenia 1/1/1997 332 1 Atrophy of spleen 2/4/2016 1 Splenectomy 3/10/2015

CODE LISTS: v2 codes need mapping to CTV3:

  1. Dysplenia Read 2 LSHTM/PRIMIS spleen_Jul19.xlsx + QOF (@hmcd by screening PNIMATRISK and also searching for "splen" and "spleen") spleen_QOF.xlsx + SNOMED to follow Note on code selection: did not include splenomegaly/cysts (not evidence of reduced function), TB, haematological malignancies (covered elsewhere)

  2. Sickle cell disease Read 2 LSHTM/PRIMIS sickle_Jul19.xlsx + QOF (@hmcd searched for sickle, scd and reviewed PPV immunosuppression at risk cluster) [sickle_QOF.xlsx](https://github.com/ebmdatalab/tpp-sql-notebook/files/4463652/sickle_QOF.xlsx + SNOMED to follow

FLEXIBILITY NEEDED BETWEEN STUDIES: None

EFFECTS ON COHORT SELECTION: None POTENTIAL BIASES: None

CLINICAL SIGN OFF & DATE:

EPIDEMIOLOGY SIGN OFF & DATE:

SHARED WITH WIDER TEAM: Yes/No

FINAL SIGN OFF DATE (and apply label)

hmcd commented 4 years ago

@CarolineMorton @alexwalkercebm added QOF for sickle - SNOMED for both to follow - did we decide re thalassaemias? (I see coeliac disease is elsewhere defined separately).

CarolineMorton commented 4 years ago

@hmcd Just to be clear, are we including thalassaemia? at present i have only included sickle cell disease

snowmed for sickle cell: snowmed-sicklecell.xlsx

snowmed for splenectomy/asplenia: snowmed-asplenia.xlsx

CarolineMorton commented 4 years ago

(1) Dysplenia and (2) Sickle Cell Disease (separate exposures)

DEFINITION: (1) Patients with asplenia or dysplenia ever recorded. (2) Patients with a diagnosis of sickle cell disease ever recorded.

Output 3 columns for each of dysplenia and sickle cell disease : 1) a binary variable denoting the presence of one of the codes at any point in the patient record (2) a string variable with the Read term for the earliest recorded code (3) the earliest date of this code

example patient_id spleen_term spleen_date sickle_term sickle_date
123 Total splenectomy 1/2/2009
4214 Sickle Cell Disease 9/4/2003
332 Atrophy of spleen 2/4/2016

CODE LISTS: v2 codes need mapping to CTV3:

  1. Dysplenia. FINAL LIST: Spleen_CTV3_FINAL.xlsx

    • Read 2 LSHTM/PRIMIS spleen_Jul19.xlsx
    • QOF (@hmcd by screening PNIMATRISK and also searching for "spleen" and "spleen") spleen_QOF.xlsx Note on code selection: did not include splenomegaly/cysts (not evidence of reduced function), TB, haematological malignancies (covered elsewhere)
    • snowmed for splenectomy/asplenia: snowmed-asplenia.xlsx
    • Reviewed by @CarolineMorton. Spleen_CTV3_REVIEWED.xlsx
      • Removal of congenital syphilis except congenital syphilis splenomegaly
      • removal of unspecified injuries to spleen, for example trauma as may not result in removal
      • removal of accessory spleen as is an extra spleen

  2. Sickle cell disease. FINAL CODE LIST: Sickle_CTV3_final.xlsx. Compiled by following process:

FLEXIBILITY NEEDED BETWEEN STUDIES: None

EFFECTS ON COHORT SELECTION: None POTENTIAL BIASES: None

CLINICAL SIGN OFF & DATE: Caroline Morton @CarolineMorton 14.4.2020 18.30

EPIDEMIOLOGY SIGN OFF & DATE: Alex Walker (@alexwalkercebm) 14/4/2020 18:56

SHARED WITH WIDER TEAM: Yes

FINAL Sign Off 14/4/2020 21:09

HelenCEBM commented 4 years ago

Looks like the high-level SNOMED codes have brought in "Excision of lesion of spleen (78412)" which should probably be removed, based on the other items we have excluded (such as cysts/injury which do not necessarily result in removal or reduced function)