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This wiki is maintained as a guide for analysts who are seeking to improve patient outcomes through better use of data for clinical care, audit and research at the Edinburgh Cancer Centre and across Scotland. If you would like to contribute please get in touch with maheva.vallet@ed.ac.uk (Edinburgh Cancer Senior Research Manager) or cancer.information@nhslothian.scot.nhs.uk
Contents
Edinburgh Cancer Centre Information Programme
The Edinburgh Cancer Centre provides comprehensive cancer care for South East Scotland, serving patients within the 4 regional Health Board – NHS Lothian, NHS Fife, NHS Dumfries and Galloway and NHS Borders. In 2014 the Edinburgh Cancer Centre began a Cancer Information Modernisation Programme. The programme focuses on obtaining improved access to cancer patient data to support service planning, delivery of better quality care and improved outcomes for patients. The ultimate aim being to deliver a world class resource for use in collaboration with national analytical partners, researchers and Scottish Government’s Innovative Healthcare Delivery Programme.
Serving a population of 1.4 million, the Edinburgh Cancer Centre has for 40 years maintained a clinical process and outcomes database that integrates with regional electronic health systems and describes the complete cancer journey. This ability to provide a comprehensive description of the clinical pathway and cancer journey is essential for robust HTA. By linking this data with modern prescribing, treatment and diagnostic databases, wider health outcomes, healthcare activity and costs can now be measured in addition to the various necessary clinical outcomes measures. The Edinburgh Cancer Information Modernisation programme is based on an update of this legacy database, using it as the foundation for a fully integrated system.
The programme is facilitated by close working with the Cancer Research UK Edinburgh Cancer Research Centre which has international expertise in Bioinformatics, Genetics and Molecular Biology applied to cancer.
Datasets
Regional Datasets
- South East Scotland Oncology Cancer (SESCD)*
- TrakCare*
- ChemoCare (SACT)*
- ARIA (Radiotherapy)*
- Bespoke audit databases
- EDGE (Clincial Trials)*
- Patient Level Information and Costing System (PLICS)
- Clinical Genetics*
*providing real-time data from live clinical systems
The South East Scotland (SES) Cancer Database
The South East Scotland Oncology Database has been populated and maintained by the Department of Oncology at ECC since it was established in 1974. The database contains a broad spectrum of data items across various stages of the cancer patient journey including diagnosis, treatment, follow-up and recurrence. It is the richest single source of cancer data in NHS Lothian and a unique facility within South East Scotland. In 2019 the database underwent modernisation, becoming the South East Scotland Cancer Database.
A data dictionary and coding manual is available for the version of the database used until 2017.
The up to date data dictionary is available on this wiki: The South East Scotland (SES) Cancer Database
TrakCare
TrakCare (InterSystems) is the nationally adopted electronic health record. Structured as a Patient Administration System, it provides epidose-structured data describing inpatient, outpatient and daycase attendances as well as radiology procedures. Within NHS Lothian it hosts the module used for cancer data entry by multi-disciplinary teams. Hospital coding (ICD-10 diagnostic codes and OPCS procedure codes) takes place within TrakCare. Radiology and pathology reports are also contained within TrakCare as unstructured or semi-structured text. Data can be extracted or reported using the BOXI Business Intelligence reporting tool, supported by eHealth in NHS Lothian. Lothian Analytical Services also maintain an Oracle server that holds a variety of extracts from TRAK.
ChemoCare (SACT)
Chemotherapy prescribing system has been in use since 2006. ChemoCare has been adopted as the standard SACT prescribing system in all Scottish Health Boards. An ongoing programme of work is harmonising the data definition across Scotland. A single ChemoCare instance is used across the SCAN Health Boards. Variables are available from the SCAN ChemoCare instance via the bespoke SCAN ChemoCare reporting tool. A data dictionary is available..
ARIA (Radiotherapy)
Radiotherapy system is the point of care software used for radiotherapy planning and delivery. Until recently data from ARIA was exported to Public Health England as part of the NATCANSAT database. This has now stopped and a regional solution for bespoke and routine data extraction is in development within the Edinburgh Cancer Centre, which provides radiotherapy services for the whole of SCAN. The Edinburgh Cancer Centre received a data dump from NatCanSAT that contains an RTDS compatible dataset from April 2012 - October 2016.
Bespoke audit databases
There are a large number of legacy and actively maintained databases designed with specific purposes in mind. An example is that maintained by the Secondary Breast Cancer Clinical Nurse Specialists service within NHS Lothian. This records the demographic and clinical details of all patients seen with secondary (stage IV) breast cancer. Similar databases are maintained by other specialist services, such as the Cancer of Unknown Primary service at the Edinburgh Cancer Centre. The majority of the data bases are simple Excel spreadsheets.
EDGE (Clincial Trials)
Is the UK national clinical trials patient database. This contains patient detains with regards to screening, approaches, participation, randomisation and withdrawal for all clinical trials operated within the Scottish Cancer Research Networks.
Patient Level Information and Costing System (PLICS)
NHS Lothian is the first Health Board in Scotland to implement its own PLICs system. PLICS uses a hybrid costing method, adhering to standardised methods to assign costs to the individual components of care episodes. Example components are nursing time, medicines cost and surgical theatre time.
Clinical Genetics
Held in isolation within NHS Lothian, the Clinical Genetics Service holds information on germline genetic testing (such as BRCA gene mutations) for local patients as well as providing testing on a national basis for specific diseases.
National Datasets
The Scottish Cancer Registry (SMR06)
SOCRATES, the main database for The Scottish Cancer Registry and has been collecting information since 1958.
For more info: http://www.isdscotland.org/Health-Topics/Cancer/Scottish-Cancer-Registry/
Tertiary referral centres and regional analysis
SMR06 identified Health Board of diagnosis separately to Health Board of residence. In an example cohort derived for breast cancer, roughly 36% of patients in SMR06 diagnosed within NHS Lothian each year are non-Lothian residents.
The Scottish Morbidity Record
Collects data on secondary care in Scotland, including inpatient, outpatient, maternity and mental health episodes.
See the SMR Data Manual on the ISD website.
SMR01 The General/Acute and Inpatient Day Case dataset collects episode level data on hospital inpatient and day case discharges from hospitals in Scotland.
Data dictionary: http://www.ndc.scot.nhs.uk/Data-Dictionary/SMR-Datasets//SMR01-General-Acute-Inpatient-and-Day-Case/
SMR99 (NRS Mortality): National Records of Scotland (NRS) classifies the underlying cause of death and up to 7 contributing causes (in terms of the International Statistical Classification of Diseases and Related Health Problems) on the basis of the information collected on the death certificate together with any additional information provided by official sources, such as the doctor who certified the death and pathologists.
NHS Lothian (Lothian Analytical Services) hold an updated file containing death data from NRS/GRO for all deaths registered in Scotland. This is held as a flat file and is also mounted on the Lothian Analytical Services Oracle database.
SMR00: The Outpatients dataset collects episode level data from patients on new appointments at outpatient clinics in all specialties (not A&E).
A&E Data: Emergency Departments and departments that provide Accident and Emergency (A&E) services submit data to ISD through the A&E datamart.
Social care (SOURCE): ***In development***
- Routine social care data collection which can cost social care activity and be linked with other routinely collected health within a single datamart called SOURCE.
- Information on Home Care services has been collected by the Scottish Executive since the 1980's by means of an annual census called the Social Care Survey.
- In 2013, the previously separate Self-Directed Support/Direct Payments survey was included in the Home Care census. Information was collected on an individual basis for each Home Care client receiving home help services, meals services and community alarm / telecare services, as well as for clients receiving Direct Payments.
- Data is usually collected with respect to the last week in March.
- Further information is available from http://www.gov.scot/Topics/Statistics/Browse/Health/SocialCareSurvey .
- Homecare datasets from 2010 to 2012 have been made available on public release: http://www.gov.scot/Topics/Statistics/Browse/Health/Data/HomeCare/HSC-Datasets-HCPRF .
- David Henderson has made available his code to manipulate and report this data: https://github.com/davidhen/social_care_open_data .
Prescribing (PIS): The Prescribing Information System (PIS) holds details of prescription items dispensed in the community, prescription details, dispenser details remuneration of drug items and patient CHI number.
SCI Store: SCI Store is an information repository for a National Laboratory Results data mart to hold clinical biochemistry data (e.g. Patient demographics, Laboratory investigation reports, Radiology reports, etc.)
NHS 24:
Scottish Ambulance Service:
GP Out of Hours:
Patient Level Information Costs (PLICs): produced to support the strategic planning of health and social care integration authorities. Data pulled in from Costbook, SMR01, SMR02, SMR04, SMR50, A&E, PIS, NRS Deaths. Cancer-specific costings are not yet included within this project.
Quality Performance Indicators (QPIs) /Cancer Audit
Quality Performance Indicators (QPIs) /Cancer Audit: The Scottish Cancer Taskforce established the National Cancer Quality Steering Group (NCQSG) in 2008 which includes responsibility for the development of small sets (approximately 10-15 indicators) of tumour specific national quality performance indicators (QPIs). The QPIs have been developed collaboratively with the three Regional Cancer Networks (NOSCAN, SCAN, WOSCAN), Information Services Division (ISD), and Healthcare Improvement Scotland.
What is Cancer Informatics?
Information technology plays a key role in fighting cancer through a growing field called cancer informatics.
Cancer informatics is where information science, computer science and health care intersect. It’s about acquiring, storing and using information about cancer most thoroughly and efficiently.
Its tools include computers, clinical guidelines, and information and communication systems. It uses information about patient physical, psychological and social characteristics ('phenotype') and their molecular characteristics ('genotype'). These characteristics are studied in relation to how patients interact with the health system and how patients are affected ('outcomes').
A key feature is the synthesizing of data about cancer in ways such as analyzing captured data, gathering evidence from clinical trials, applying information into clinical practice, evaluating outcomes of changes in clinical practice, and generating new hypotheses for investigation.
The Edinburgh Cancer Informatics Programme is striving to use methods in cancer informatics to implement a “rapid-learning system for cancer care.” The “rapid-learning’ comes from the healthcare system being able to keep itself constantly informed on how it is affecting the patients it cares for.
Cancer informatics is a broad field, getting deeper and more complex as medical research and information technology progress. The field is all about collaboration, not just among physicians and researchers but between doctors and health IT professionals and patients and the public.
Patient perspectives
Making better use of NHS data provides huge opportunities to benefit patients and the public, whilst respecting patient confidentiality. There is a strong and united patient voice in the UK guiding the use of data for this purpose. #usemydata provides some useful insight. The safe use of data in Scotland is governed by the Caldicott Guardians, operating through the Public Benefits and Privacy Panel.
Access to data linked to tissue samples
Anonymised data is available for research linked to tissue samples under the NHS Lothian NRS Bioresource link
General Guidance for Analysts
Defining a cohort
New diagnoses of cancer are recorded in the Scottish Cancer Registry (SMR06). Cancer statistics are usually reported over the range of ICD-10 codes that define invasive cancer C00-C96. It is common to exclude C44 (non-melanoma skin cancer) because it is non-life threatening, it is poorly or inconsistently recorded and there are large numbers of cases. The registry website contains more information http://www.isdscotland.org/Health-Topics/Cancer/FAQ .
See cancer type specific sections of this wiki to understand how to derive a cohort of patients diagnosed with a specific type of cancer.
Patient and population characteristics (phenotype and genotype)
Defining the characteristics of patients with breast cancer using the Scottish Morbidity Record
- Demographics: Age, gender, Deprivation (Scottish Index of Multiple Deprivation; SIMD),
- Geography: Rurality, Health Board of Residence, Health Board of Diagnosis, Health Board of Treatment
- Comorbidity: Charlson score (continuous), Charlson variables (17; binary)
- Stage: AJCC Stage, TNM, Tsize, Nnumber, grade
- Molecular subgroup: ER, HER2
- Treatment: Surgery, Chemo, RT, Hormone therapy, Biological/other therapy
Deprivation
A project conducted by ISD and funded by Macmillan in 2017 provides an excellent description of methods suitable for the characterisation of patient populations by SIMD. It presents an overview of methods for studying the association between survival and deprivation. See the project page published by Macmillan for full details.
By default for cancer analysis, we are using the ISD preferred method for ranking and categorising by Scottish quantiles.
Staging
T and N stage can be clinical (assessed by clinical or radiological evaluation) or pathologically (by microscopic assessment following surgical excision). Clinical staging follows universal definitions across all diagnosed cancer following the manual produced by the American Joint Committee on Cancer.
Outcomes
Toxicity
Toxicity data collected in clinical trials conforms to the Common Terminology for Adverse Events (CTCAE) definitions. In routine care, toxicities are graded along the same scale of 0 to 5. Clinical teams attempt to align their toxicity reporting as closely as possible with CTCAE, but there may be some drift from these precise definitions. Within South East Scotland, patients undergoing Systemic Anti-Cancer Therapy are assessed for toxicity prior to each cycle of treatment and the graded toxicities are recorded in coded form in ChemoCare.
Disease-specific survival
Defined as: The percentage of people in a study or treatment group who have not died from a specific disease in a defined period of time. The time period usually begins at the time of diagnosis or at the start of treatment and ends at the time of death. Patients who died from causes other than the disease being studied are not counted in this measurement.
Assignment of cause of death is complex and guided by ICD-10 standards: http://apps.who.int/classifications/icd10/browse/Content/statichtml/ICD10Volume2_en_2010.pdf
Consideration needs to be given to competing risks in cohort or research studies (candidate methods include Fine and Gray or Cox subdistribution models). For epidemiological interpretation, consider relative survival or net survival.
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