Sites in Genetics of Endocrine Tumours Study

Korbonits Lab meeting

Kesson Magid

11/10/23

The Problem

Finding patients from Barts

run a search for “Barts” in variable site_old

  1. Barts
  2. Barts Royal London Hospital
  3. Centre For Endocrinology, William Harvey Research Institute, Barts And The London School Of Medicine, Queen Mary Univ~
  4. Department Of Endocrinology, St. Bartholomew’S Hospital, London, Uk
  5. Department Of Endocrinology, St. Bartholomew’S Hospital, London, Uk
  6. Kings/Barts
  7. St Batholomew’s Hospital
  8. Queen’s Square (Surgery) / St Bartholomew’s (Presentation)
  9. Queen’s Square (Surgery) Barts (Endo)
  10. St Bartholomew’s Hospital
  11. St Barts
  12. Uclh Queen’s Square / Bart’s
  13. Uclh Queen’s Square / St Bartholomew’s

Data cleaning objectives

  • Harmonise site names

  • Assign city, country

Data cleaning objectives

  • Harmonise site names

  • Assign city, country

Where there were different spellings or capitalisation of site names they’ve been rationalised. This reduced the total number of site entries by 70 (from 464 to 394).

Data cleaning steps

Create a key document

  1. Export all names of sites (n = 700)

  2. Match to a linking variable

  3. Update data using link

Data cleaning results

This reduced the number of missing entries:

  • Country: filled 1983 (from 2570 to 587)
  • City: filled 2230 (from 4561 to 2328)
  • Clinician_1: filled 56 (from 2144 to 2088)

Data cleaning results

This reduced the number of missing entries:

  • Country: filled 1983 (from 2570 to 587)
  • City: filled 2230 (from 4561 to 2328)
  • Clinician_1: filled 56 (from 2144 to 2088)

This will help on the next step, which is to produce a comprehensive list of the source of samples/data/recruitment of all patients on the study that we will include in the GWAS or other analyses.

UK Cities

Top 20 UK GOET Sites by city

London      2714
Newcastle    310
Manchester   227
Leicester    223
Plymouth     111
Leeds        107
Belfast       84
Cardiff       77
Norwich       66
Birmingham    64
Cambridge      63
Liverpool      46
Yeovil         41
Cumbria        25
Bournemouth    24
Oxford         22
Aberdeen       21
Bristol        20
Sheffield      17
Hull           15

Next steps

Address missing data

  • Site (7537 filled, 2423 missing)
  • City (7482 filled, 2478 missing)
  • Country (9260 filled, 700 missing) Perhaps best to go work from country first, then city, then site

Update linking document

  • Clinician (PI) details where available