Live demo of importing and analyzing eGFR data in -

CKD v4.4.2

Dr Darren PowellDr Louise Hassall

St Helens and Knowsley & Southport and Ormskirk NHS Trusts

Background

• Our Pathology dept serves 2 trust= 4 CCGs, 120 GP = 600K popln.

• Live with -CKD reporting since Dec 2016.

• Initially started with v 2.2 before switch to v4.x earlier this year.

• Perform our run every Wednesday: Analyse date from previous Weds to Tues.

• Takes approx. 2 hours (now that we are used to the process)

• Follow the HoE Birm 2-search system: 1) 66-120yrs, then 2) 18-65 yrs

• Add approx. 13k new results per week

• Screen approx. 350 graphs per week, marking 50-60.

• When setting up we also imported historical eGFR data from our retired Clinisys ‘Labcentre‘ Lims. Originally imported everything (9 years), but then scaled back to 5 years (size and speed)

Our PC Setup• Labsystem = CSC Telepath (v2.2) – we run a custom gather and

print to a .txt file.

• We prepare the data in Excel – to correct some location codes, tweak the location names, and missing eGFR units

….Will show shortly. ->Saved as a CSV file.

• We work cross site so have -CKD installed on different PCs on the two sites:

• This requires 4 installs of -CKD : 2 PC user accounts x 2 PCs.

• N.b need to setup a copy of the report template for each user account on Windows.

• I keep a copy of our config files and report template separate to facilitate installation and testing.

Our BD Setup• We use a MS-SQL database centrally hosted on a trust MS SQL server that is

accessible for either site.

• MySQL is the preferred method.. (robust, secure, auto backed up)

• But….if starting from scratch I would consider the ‘SQLlite option’ located on our shared Pathology drive, as would remove the delays dealing with my trust IT.

• The SQLlite DB resides as standalone folder/file so can be easily manually wiped/backed-UP/restored. Removing unwanted data from a DB is very tricky, and getting my IT to wipe my SQL DB was a pain.

• My MS SQL DB started to slow down as it filled up over time….my IT team were able to run standard optimisation tools…I don’t know if these exist or are needed for SQLlite??

• If started on SQLlite and then moved to MS SQL, would have to reimport ALL and

lose graph mark history.

Gathering and Exporting Data from the LIMS (Telepath)

Simple gather:Picks up eGFR ( both MDRD and CKD-EPR (Apr 16->) results

Column Data Type

SURNAME varchar(255)

FORENAME varchar(255)

SEX varchar(1)

DATE OF BIRTH date

HOSPITAL NUMBER varchar(17)

NHS NUMBER varchar(10)

LOCATION varchar(100)

LOCATION TYPE varchar(1)

CLINICIAN varchar(255)

SPECIMEN IDENTIFICATION varchar(17)

TEST DATE date

RESULT decimal(10, 3)

UNITS varchar(15)

POST CODE varchar(17)

Management Stats Groups Codes

AE Accident & Emergency

CM Community Medicine

DC Day Care

FI Forensic Inpatients

GP General Practice

GPF GPF no longer in use

IP In Patient

OH Other Hospitals' Pts

OP Out Patient

PI Paediatric Inpatient

PM Post Mortem

DB Specification

Content of our LIMS (Telepath) data gather output:

Hard bit: getting all the required data out of the system..

Requires -CKD to be installed

(Allowable Location Types in = I, O, R, X)

Using the Location code Mapping Table (v4.x ‘settings’) to convert my LIMS Location codes to the expected ones

(I,O,R,X).

Requires -CKD to be installed

(Allowable Location Types in = I, O, R, X)

Using the Location code Mapping Table (v4.x ‘settings’) to convert my LIMS Location codes to the expected ones

(I,O,R,X).

Management Stats Groups Codes

AE Accident & Emergency

CM Community Medicine

DC Day Care

FI Forensic Inpatients

GP General Practice

GPF GPF no longer in use

IP In Patient

OH Other Hospitals' Pts

OP Out Patient

PI Paediatric Inpatient

PM Post Mortem

Things to speed things up

• SQL database maintenance:

• Have approx. 3 million entries (adding :13K results per week)

• After experiencing some slowdowns, suggested getting a weekly maintenance procedure (reindexing the DB based on NHS number).

• Had a big effect, now scheduled for every Friday AM.

• Work with a dual desktop monitor system. Can more easily view graphs and interrogate results on the labs system. See over.

• Use the ‘Full eGFR Results table’ to warn if the patient has since been admitted (thus Marking not required), or if previous hospice results.

Our report template• Very similar to original, just added logo, and tweaked formatting.• Advice text…see following slide

Path Admin staff requested to have BOTH the location CODE and the location NAME on each report to help with the sorting and posting…

Our report template

Our report template

• Advice text was written with the ance of the Regional Renal lead.• We send out the same message to both groups of users.• Suggest that any initial questions about the scheme are directed

directly to myself or Louise. ….earlier version was not as clear and people called the office.

On to the Demo…..

going forwards..• Although we will be seeking money from the CCGs to continue the scheme,

our HOD has agreed to fund it.• Got the support from the trust medical director who is keen for it to

continue.• The process has been absorbed into our weekly DB duties.• Path admin staff have (begrudgingly ) accepted it.• We wish to switch to electronic alerts and include a line asking for a

suitable GP Practice email address.• Explore Kettering’s approach of using the Trust TIE to send results directly

to the MS SQL and potentially bypass the manually data loading.

Final thoughts

• If you are not yet live due to IT delays with a MS SQL DB, consider the alternative SQLlite.

• If you are not on V4.x yet , I strongly suggest you do so.

• Much faster and easier to use….big evolution over v2.x

• Has greatly improved and customisable alerts which are meaningful to the clinician.

• We did a mini validation exercise when moving over, but mainly it was previously untested by other sites.

n.b, you can expect slightly different numbers in each search due to date parsing differences in v2 vx v4x.

• Overall, it has been well received by our GPs, and other clinicians.

• We did get a few phone calls at the start from GPs who had not read or understood the alert advice, but has lessened now we have a customised alert with v.4

• Hope to perform an audit of our GP satisfaction and request formal feedback next year.

Any Questions?