QRISK3

Endeavour Predict is a manufacturer of EP QRISK3 Engine which is the implemenation of QRISK3 by Endeavour Predict.

The EP QRISK3 Engine, with both a Web API and local run time components are now registered as a class 1 device with the MHRA and available for use

Background

Information about the research and algorithms that resulted in QRISK3, as well as the free to use Web site can be viewed at https://qrisk.org and a related presentation, a CVD lifetime risk at https://qrisk.org/lifetime/index.php

Predict Services

QRISK3 risk score can be calculated using Endeavour Predict services, which consist of:

1. A set of Web based APIs for submitting requests for a prediction and receiving a response, the response including a risk score, and other score specific information for example in QRISK3, a heart age , as well as information relating to the calculation of the scores.
2. A local run time C# or Java jar version for integration into local systems that prefer not to use a web UI.
3. A set of FHIR APIS to enable system suppliers to know which Snomed-CT concepts should be used when deriving information from records. These are part of the Endeavour information model services.
4. A REST API for deriving a Townsend deprivation score from a post code, the Townsend score being then submitted as part of the QRISK request payload.

Concept (Value) sets and FHIR API

Concept sets for use in QRISK3 can be seen in the Endeavour Information manager at

https://im.endeavourhealth.net/#/directory/folder/http:%2F%2Fapiqcodes.org%2Fqcodes%23QPredict_331

In line with FHIR an semantic web standards, each set is given a unique IRI and it is the IRI that is used as identifiers in the API call

Alternatively, the concept sets can be downloaded from the IM application in excel CSV , or TSV

Within Endeavour each concept is given a unique identifier or IRI in line with semantic Web. Users will be more familiar with the use of the concept's code and this is provided as well as maps to alternative code schemes.

the concept sets are available as FHIR value sets at the self sign up developer portal

https://dev.endeavourpredict.org/

The concepts sets contain subsets so that recursive calls can be made to obtain each set. Alternatively, using the $expand operation, the entire subset can be obtained as one.

APIs (Web and local)

A developer portal for qrisk3 is available at https://dev.endeavourpredict.org/apis

The algorithms are available over the internet via REST API calls or a locally deployed .NET assembly, or a locally deployed Java jar. In all 3 variations the input format (JSON) and parameters are the same and the result format (JSON) is the same. Consequently suppliers using local versions may use the developer portal to test input and output formats.

When using a locally deployed implementation, a test pack SDK is provided to enable unit and integration testing by end suppliers.

Source code

The open source code available under Lesser General Public License on the https://qrisk.org/src.php

Please note that the use of QRISK3 (as a registered trademark) is not available to be used under the LGPL license as this trademark is owned by EMIS and Nottingham University and a license to use is required. Endeavour-Predict has a license and is able to sublicense along with the deployed implementation under commercial or academic terms.

Intended use

EP - QRISK3 Engine is a clinical decision support tool intended to facilitate individualised discussions between medically trained professionals and patients about their individual risk of heart attacks or stroke taking account of their demographic and medical profile.

This will enable shared decision making, allowing patients to understand their risk and discuss actions that could be taken in the context of other important factors to reduce their risk.

EP - QRISK3 Engine has been developed for both public health purposes as well as individual therapeutic or health care decisions.

EP - QRISK3 Engine has been developed so that it can either run as a standalone process, with data being submitted and results returned in batch file format, or it can be integrated as a component or module to an interactive web-based tool, to allow data to be inputted and processed on a single individual at a time.

It is therefore also intended that EP - QRISK3 Engine will be licensed to other medical device manufacturers, so they can produce their own websites/front ends including QRISK3 Engine as a component.

Safety information and cautions

EP- QRISK3 Engine cannot take the place of clinical assessment. No medical decision should be based solely on results provided by the risk calculator. This is a labelled misuse of the QRISK3 Engine.

When developing implementations of EP- QRISK3 Engine, licensees should review relevant research paper to ensure that implementations and any system generated recommendations to clinicians/users based on the output is in line with the original intended use. Licensees may be required to CA or CE mark individual implementations as medical devices depending on the output/decision provided by the software based on a particular risk score. This may require additional clinical investigations and may result in being a higher class of device than EP-QRISK3 Engine.

Clinicians are expected to apply their own clinical judgement to further risk stratify patients and are not expected to rely solely on the output from QRISK3® (via licensed implementations) in order to appropriately manage and advise their patients regarding their risk.

Instructions for use

The REST API instructions are available at a Swagger at https://dev.endeavourpredict.org/apis

To the local batch processor the instructions for Windows are:

1. Unzip the published pack to any folder
2. Unzip the test data to another folder

To test

1. Take a copy of the test data and place in another folder
2. using the windows command line execute the EP_QRisk3.Batch.exe with a parameter pointing to the test folder
3. Note that the output is regenerated as output files. The can, if wished be compared against the original provided result files as they should be identical

To run

1. Generate source data as JSON files in the format as provided (which is the same as the API format)
2. Using the command console, execute the EP_QRisk3.Batch.exe with a parameter pointing to the source folder.

Query Rules for health records

Systems may have access to longitudinal health records, in particular those held in General Practice. In that case those systems may elect to query the health record data in a way that provides likely values for the variables, passed to the function as parameters to the QRISK function.

In this case, a set of query criteria and rules are applied to the record entries and the values of the variables derived from those entries. These are then presented to a user for confirmation or amendment before being submitted via the API.

It is strongly recommended that for any individual decision, or when an entry of a risk score is into a record is being considered, that each set of assumptions are confirmed by the user. However, purely automated calculations may be used for population based risk stratification.

Reference date

Scores may be calculated in real time or retrospectively. The reference date (current date or past date) is used for all time dependent values, which means values as they would have been on the reference date. For example when looking for dates within 6 months this means 6 months prior to, or at the time of, the reference date and all entries subsequent are ignored.

Patient inclusion criteria

This section documents the criteria for a person suitable for the application of QRISK3

• Aged between 25 and 84 inclusive at the reference date

• Free from a diagnosis of cardiovascular disease (qr: group 411 see below) on or before the reference date

Independent variables as function parameters

QRISK® operates as a function whose parameters represent independent variables. The API accepts these arguments as JSON key value pairs (or lists) in the payload of the request.

The values of those variables, when used in the algorithm are derived in one of two ways

a) By direct entry by a user

b) By a query of a health record.

When passed into the algorithms as arguments to the function, the values are presented either enumerators (e.g. heavy Smoker) as a double (e.g. BMI), an integer (e.g. Systolic BP) or , a boolean true or false. The enumerator text values are documented in the API swagger and are the same for the local run time

If variables are unknown (missing) or their values are out of range, the algorithm may either reject the request, provide a default value for the parameter, or adjust an out of range value to an outer limit. The way the algorithm handles these parameters are documented below in the relevant parameter.

Health records contain entries that have a property of a main concept (e.g. a systolic blood pressure), an effective date (the date of relevance to the observation or action), and a numeric value. For the purposes of these rules, concepts are grouped into named sets.

sets can be examined at https://im.endeavourhealth.net/#/directory/folder/http:%2F%2Fapiqcodes.org%2Fqcodes%23QPredict_331

Each concept set is universally identified with an RDF IRI (which is in the format of a URL) and the base iri namespace for Q concept sets is

"http://apiqcodes.org/qcodes#QCodeGroup_" thus in the below table the numbers following this base IRI are used for brevity

When querying records it is assumed that a reference date is used and that entry dates are relative to the reference date and that any entry after the reference date is ignored

Input parameters needed to calculate a QRISK3® score and their handling are as follows:

Parameter	Type	Values	Description and query definition
Row id	integer		Used by the client as a reference when a batch API is used. i.e. returned by the result. It has no scope beyond the API request/response
Age	integer		Age of the person in years at the reference date
Gender	Character	Male - M Female - F	The Gender of the patient. Note that the risk following gender transition is unknown, and thus a clinical judgement as to whether to use the category of male or category of female.
Cardiovascular disease	boolean	true false	Cardiovascular disease prior to the reference date This is an inclusion criteria and should therefore be false. A valid RISK score requires absence of cardiovascular disease. Query defined as Condition with concept of code group 411
Atrial fibrillation	boolean	true false	Atrial fibrillation at any time prior to reference date. QRisk does not differentiate a single one off AF event from chronic or intermittent AF. Clinical interpretation may be required for those with a single event many years ago. Query defined as Observation with concept of code group 24
Erectile impotence	boolean	true false	A recording in a health record Erectile dysfunction at any time prior to reference date or treatment with drugs for dysfunction with at least 2 issue, the latest of which is within 28 days of the reference date. Note that this factor is associated with a diagnosis as recorded in GP health records, and may or may not be valid as a response to a question. Query defined as Condition with code group 59 or ( 2 or more Prescriptions for code group 1683 the latest of which has date within the last 20 days )
Atypical anti psychotics	boolean	true or false	Second generation ‘atypical’ antipsychotic - prescribed two or more issues in the previous 6 months (includes amisulpride, aripiprazole, clozapine, lurasidone, olanzapine, paliperidone, quetiapine, risperidone, sertindole, or zotepine). Query defined as 2 or more Prescriptions for code group 1169 within the last 6 months
Systemic corticosteriods	boolean	true or false	Patient taking systemic corticosteroids. Query definition 2 or more prescriptions for code group 1194 in the last 6 months
Migraine	boolean	true or false	Diagnosis of migraine i.e. a diagnosis of migraine recorded in health records. Self reported migraines not resulting in a health record entered diagnosis is not evaluated. Query definition Condition with concept group 39
Rheumatoid arthritis	boolean	true or false	Diagnosis of Rheumatoid arthritis. Query definition is Condition with concept group 58
Chronic renal disease	boolean	true or false	Diagnosis of chronic renal disease. Query definition is: Condition with concept group of 322
Severe mental Illness	boolean	true or false	Diagnosis of severe mental illness (psychosis, severe depression, manic depression, schizophrenia). Query definition is Condition with concept group 3187
Systemic lupus erythematosus	boolean	true or false	Diagnosis of Systemic Lupus erythematosus. Query definition is : Condition with code group 70
Treated hypertension	boolean	true or false	Diagnosis of hypertension at any time in the patient’s records AND On antihypertensive treatment if 1 or more prescriptions within the last 6 months. Query definition as follows Condition with concept group 21 and 1 or more Prescriptions for code groups 740, 751, 759, 760, 765 within the last 6 months
Body mass index	double	The most recently recorded body mass index within the last 5 years. Query definition is Latest Observation with code group 200 within the last 5 years Out of range values handled by the engine are <18 is set to 18, >47 is set to 47
Diabetes Category	Enumerated	None, type1, type2	Diagnosis of diabetes mapped to a category. Note that resolved diabetes or well controlled diabetes) is not accounted for in the algorithm. Judgement should be used as to how the risk is applied. Query definition as follows From latest diagnosis of code groups 1913,2411 Map code group 1913 Type1 Map code group 2411 Type2
Ethnicity	Enumerated	NotRecorded, British, Irish, OtherWhiteBackground, WhiteAndBlackCaribbeanMixed, WhiteAndBlackAfricanMixed, WhiteAndAsianMixed, OtherMixed, Indian, Pakistani, Bangladeshi, OtherAsian, Caribbean, BlackAfrican, OtherBlack, Chinese, OtherEthnicGroup, NotStated	Most recent ethnicity. Query definition is latest entry for code groups 17071, 17072, 17073, 17074, 17075,17076, 17077, 17089, 17079, 17080, 17081, 17090, 17985,17086, 17087) Maps 17071 White british 17072 White Irish 17073 Other White Background 17074 White & Black Caribbean 17075 White & Black African 17076 White & Asian 17077 other mixed 17089 Indian 17079 Pakistani 17080 Bangladeshi 17081 Other Asian 17090 Caribbean 17083 Black African 17091 Other Black 17985 Chinese 17086 Other ethnic group qr:17087 Not stated and not classified
Family history of Coronary heart disease	boolean	true or false	Family history of coronary heart disease in a first degree relative under the age of 60 years. Query definition is Entry for concept group 404
Total cholesterol HDL ratio	double		The latest ratio of total serum cholesterol/HDL recorded in the last 5 years. The ratio is either directly directly recorded can be calculated using total cholesterol divided by hdl. Query definition is: latest Observation with concept group 16 (TC) Latest concept group 367 (HDL) Latest concept group 405 (TCHDL) If TCHDL effective date > TC effective date OR TCHDL effective date >HDL effective date then value= TCHDL numeric value else if TC effective date > TCHDL AND HDL effective date >TCHDL effective date then value = TC / HDL else value = null Handling of out of range values by calculator <1 is set to 1, >12 is set to 12
Smoking category	Enumerated	NonSmoker, ExSmoker, LightSmoker, ModerateSmoker, HeavySmoker, NotKnown	The most recently recorded smoking status with 5 levels This categorisation has one group for ex-smokers rather than trying to distinguish between ex light, ex moderate and ex heavy smokers. This categorisation does not distinguish between cigarette/cigar and pipe smokers Special consideration should be given to records that contain both numeric values for the number of cigarettes smoked, and concepts that categorise into light moderate or heavy. The logic on non smoker is that from the entry of the most recent if it has a numeric value or if there other codes on the same day with numerics take the numeric value on the same day as the most recent, unless the most recent is non smoker Query definition is Latest (MOSTRECENT) Observation with concept group,2239 -(NONE), 2238 (EX) 2244 (LIGHT), 2242 (MODERATE) qr:2243 (HEAVY) and numeric value is NULL as NOVALUE If most recent is NOVALUE (as MOSTRECENT) if most recent HAS VALUE effective date= MOSTRECENT effective date // non value and value on same date! - - then value is numeric map of HASVALUE numeric value else - - value is concept map of NOVALUE concept else if most recent is HAS VALUE - - value is numeric map of MOSTRECENT numeric value else no record value is null Map 2239 None smoker 2238 Ex Smoker 2244 light smoker 2242 Moderate smoker 2243 Heavy smoker
Systolic blood pressure	integer		The most recent systolic blood pressure within 5 years. Query definition is Numeric value of Most recent Observation with concept group 198 within the last 5 years and numeric value not null Handling of values out of range <70 is set to 70, >210 is set to 210
Standard deviation of systolic blood pressures	double		The SAMPLE style Standard deviation of all of the available systolic blood pressures prior to the reference date recorded in the last 5 years. Note that EP QRISK3 will calculate the spb 5 from a list of values. Query definition is Observation with concept group 198 and numerivc value not null Return Standard deviation (sample) (Systolics) or list of values
Townsend score	double		The Townsend score associated with the output area of a patient’s postcode based on the 2001 census data. Available via API Default handling of unknown is 0 (the mean of the national scores)