A practical guide for pharma and patient support programmes, insurers and employers, and clinics and laboratories on the data decisions that determine whether an autoimmune programme can support patients well and show outcomes that hold up.
Autoimmune conditions are far more common than many people realise. A study of 22 million people in the United Kingdom found that around one in ten had at least one of 19 autoimmune disorders, including 13.1% of women and 7.4% of men.1 Around the world, an estimated 17.6 million people live with rheumatoid arthritis,2 at least 100 million with psoriasis3 and 3.41 million with systemic lupus erythematosus.4 Inflammatory bowel disease, once seen mainly in Western countries, has been rising in newly industrialised countries since 1990, including across Asia.5
These are long-term conditions that come and go in flares. Care is often shared between several specialists, and treatment frequently includes biologic medicines and biosimilars given over many years. That is why patient support programmes for autoimmune conditions are among the largest in pharma, and why their value depends on showing what happens to patients over time, not at a single visit.
We wrote this guide for three groups of readers. If you lead a pharma-supported or patient support programme, it sets out what your data needs in order to support patients well and to show real-world outcomes. If you work for an insurer or employer funding these treatments, it explains what good programme data looks like and what to ask for. If you run a clinic or laboratory, it covers how to keep a patient's record coherent as treatments, results and specialists change. The twelve points apply to all three, and where the emphasis differs, we say so.
Consider a woman in her thirties with psoriatic arthritis. Her rheumatologist and dermatologist each keep their own notes. Her blood tests are done at whichever laboratory is closest that month. Her biologic is delivered through a patient support programme, injected at home, and switched to a biosimilar after a change in funding. Her tuberculosis screening result sits in a hospital system she no longer visits, and the only record of how her joints and skin have felt between appointments is in an app on her phone.
Each source holds part of the story. The value comes from bringing them together in a way that stays accurate over years of treatment.
The twelve points below are grouped into four themes: getting the clinical picture right, making the data usable, connecting the longer story, and building for trust and scale. After them, we set out what to capture for each of the four main conditions.
Every autoimmune condition has recognised ways of measuring how active the disease is, and programmes that invent their own measures struggle to compare patients or show outcomes. For rheumatoid arthritis, the American College of Rheumatology (ACR) recommends five measures: the 28-joint Disease Activity Score (DAS28) using either the erythrocyte sedimentation rate (ESR) or C-reactive protein (CRP), the Clinical Disease Activity Index (CDAI), the Simplified Disease Activity Index (SDAI), the Routine Assessment of Patient Index Data 3 (RAPID3) and the Patient Activity Scale II (PAS-II).6 Psoriasis, psoriatic arthritis, inflammatory bowel disease and lupus each have their own established measures, which we list in the condition section below.
The version matters as much as the measure. The standard DAS28 thresholds are below 2.6 for remission, 3.2 or below for low activity and above 5.1 for high activity.7 Yet in early rheumatoid arthritis, DAS28-CRP values were found to be consistently lower than DAS28-ESR values, and the authors concluded the two should not be used interchangeably.8 A programme that pools the two without labelling them may report more patients in remission than there really are.
What good looks like: each score stored with the instrument, the version, the date, who recorded it (clinician or patient) and the component values behind it, so it can be recalculated or compared later.
Matters most to: Pharma programmes, Clinics and laboratories
Flares are central to how patients experience autoimmune disease, and many programmes report them as an outcome. There is no single agreed definition. When the Outcome Measures in Rheumatology (OMERACT) group reviewed how flares were defined in rheumatoid arthritis, it found definitions were quite variable, and noted that a measure to assess worsening of disease had yet to be developed.9
In practice, a flare may be recorded because a patient called the programme nurse, because a clinician increased steroids, because a disease activity score rose, or because the patient was admitted to hospital. Counting all of these as the same event produces numbers nobody can interpret.
What good looks like: a written, operational flare definition agreed before the programme starts, with the source of each flare signal recorded separately (patient report, score change, steroid course, admission).
Matters most to: Pharma programmes, Insurers and employers
Laboratory markers play different roles in autoimmune care, and a record should know the difference. Some are used mainly for diagnosis or classification. For example, the 2019 European Alliance of Associations for Rheumatology (EULAR) and ACR classification criteria for lupus require an antinuclear antibody (ANA) at a titre of at least 1:80 as the entry criterion.10 Others are used to monitor disease over time. In inflammatory bowel disease, the STRIDE-II treat-to-target recommendations prioritise normalisation of CRP and faecal calprotectin as treatment targets.11
Inflammatory markers can also rise for reasons other than the autoimmune disease itself, such as an infection, which is a particular concern in patients on immunosuppressive treatment. A tool that reads every rise in CRP as a flare will send the wrong message to the patient and the clinician.
What good looks like: each marker tagged by its role (diagnostic, monitoring or safety) and shown alongside symptoms, recent infections and treatment changes rather than as a stand-alone alert.
Matters most to: Clinics and laboratories, Pharma programmes
For most autoimmune programmes, the treatment history is the heart of the dataset. Patients may start on a conventional medicine such as methotrexate, move to a biologic, switch to a biosimilar, and later change to a biologic with a different mechanism. In the European Union, the European Medicines Agency (EMA) and the Heads of Medicines Agencies stated in 2022 that biosimilars approved in the EU are interchangeable with their reference medicine, while decisions on substitution at the pharmacy remain with each member state.12 In the United States, the Food and Drug Administration (FDA) designates some biosimilars as interchangeable, which, depending on state pharmacy laws, allows substitution without the prescriber's involvement.13
An illustrative treatment journey. Without a structured reason for each change, loss of response and a non-medical switch look identical in the data.
What makes this history useful is the reason behind each change. A switch because the treatment stopped working means something very different from a switch driven by funding, supply, patient preference or pregnancy planning. Without the reason, a programme cannot tell loss of response from a change in the tender.
What good looks like: each product recorded as its own treatment episode with active ingredient, brand, dose, route, start and stop dates, and a structured reason for each change (for example non-medical switch, primary non-response, loss of response, intolerance, funding or supply gap, pregnancy planning).
Matters most to: Pharma programmes, Insurers and employers
Before a biologic starts, several checks need to be in place. The 2022 EULAR recommendations on infections in autoimmune inflammatory rheumatic diseases advise screening for latent tuberculosis (TB), with interferon-gamma release assays preferred over the tuberculin skin test, and defining hepatitis B status before treatment begins.14 This matters especially in Asia. According to the World Health Organization (WHO), around six in ten of the world's new TB cases in 2024 were in its South-East Asia and Western Pacific regions.15
Vaccination is part of the same picture. EULAR recommends assessing vaccination status every year and giving vaccines preferably before planned immunosuppression, and says live attenuated vaccines may be considered with caution.16 These results often sit in a hospital, clinic or public health system separate from the one where treatment is managed.
What good looks like: screening and vaccination results held in the same record as treatment, with test type, result, date and source, and reminders when repeat checks are due.
Matters most to: Clinics and laboratories, Pharma programmes, Insurers and employers
Patients on long-term treatment have regular blood tests, often at more than one laboratory. CRP alone may be reported in milligrams per litre (mg/L) or milligrams per decilitre (mg/dL), depending on the laboratory, and the two differ by a factor of ten.17 Reference ranges vary, and the same test can appear under several different names. Routine safety bloods, such as blood counts and liver tests for patients on methotrexate, add to the volume.
In inflammatory bowel disease, drug levels and anti-drug antibodies are increasingly part of the record. The American Gastroenterological Association (AGA) suggests reactive therapeutic drug monitoring for patients with active disease on anti-tumour necrosis factor (anti-TNF) treatment, and the interpretation depends on both the drug level and the antibody result.18
What good looks like: every result kept with its original value, unit, reference range and laboratory, converted to a consistent unit for analysis, mapped to medical coding standards, and traceable back to the original report.
Matters most to: Clinics and laboratories, Pharma programmes
Autoimmune care rarely sits with one clinician. A patient with psoriatic arthritis may see a dermatologist and a rheumatologist. A patient with inflammatory bowel disease may also have joint or eye symptoms. A patient with lupus may be followed by rheumatology, nephrology and dermatology. Each keeps its own notes, in its own system, and often uses its own measures.
When these records are not joined up, the programme sees only the part of the patient that happens to be in its own system, and important changes, such as a new treatment started by another specialist, go unnoticed.
What good looks like: letters and notes from every specialist brought into one longitudinal record, structured so that diagnoses, treatments and measures from each can be read together.
Matters most to: Clinics and laboratories, Pharma programmes
Much of what matters in autoimmune disease happens between appointments: pain, fatigue, stiffness, skin symptoms, bowel symptoms and the ability to work and look after a family. Validated patient-reported outcome measures exist to capture this in a comparable way. RAPID3 is one of the ACR's recommended disease activity measures in rheumatoid arthritis.6 For physical function, the Health Assessment Questionnaire Disability Index (HAQ-DI) remains widely used, although the ACR's 2019 review rated it inconclusive and recommended PROMIS Physical Function 10a, HAQ-II and the Multidimensional HAQ instead.19 The Dermatology Life Quality Index (DLQI) is used in skin disease,20 and the Inflammatory Bowel Disease Questionnaire (IBDQ) in bowel disease.21
Across Asia, programmes also need validated translations and a realistic cadence. Long questionnaires completed every day tend to lose patients, while shorter structured check-ins at regular intervals usually produce better data.
What good looks like: a validated instrument in a validated language version, scored consistently, collected at an agreed cadence, and stored alongside clinician measures.
Matters most to: Pharma programmes, Insurers and employers
Biologic treatment is associated with a higher risk of serious infection. A meta-analysis in rheumatoid arthritis found that, compared with traditional disease-modifying medicines, standard-dose biologics were associated with an odds ratio of 1.31 for serious infection, and high-dose biologics with 1.90.22 Infections are also a common reason for pausing treatment, which affects every outcome a programme reports.
Most pharma-supported programmes also have adverse event reporting obligations. When safety information is captured in free-text call notes, it is easy to miss and hard to analyse.
What good looks like: infections and other safety events recorded as structured, dated events with severity, treatment and outcome, linked to any treatment pause, and routed to the right reporting process.
Matters most to: Pharma programmes, Insurers and employers, Clinics and laboratories
Autoimmune diseases affect women more often than men,1 and around 90% of people with lupus are women.4 Many are diagnosed during the years they may be planning a family, which makes pregnancy one of the most important points in the treatment record.
Guidance here is specific. EULAR advises that methotrexate must be stopped before conception,23 with the ACR advising one to three months beforehand.24 In lupus, EULAR recommends hydroxychloroquine before conception and throughout pregnancy.25 EULAR's 2024 update says TNF inhibitors may be used throughout pregnancy.26 A programme that cannot see pregnancy plans, treatment changes around conception and outcomes after birth is missing one of the moments when support matters most.
What good looks like: pregnancy intentions, pregnancies and outcomes recorded with care and consent, linked to treatment changes, with the record continuing through pregnancy rather than pausing when the patient leaves a programme's usual pathway.
Matters most to: Pharma programmes, Clinics and laboratories
Programmes are increasingly asked to show real-world outcomes rather than activity numbers such as calls made or doses delivered. The strongest outcomes follow recognised treatment targets: remission or low disease activity on a validated score in rheumatoid arthritis; clinical remission and endoscopic healing in inflammatory bowel disease under STRIDE-II;11 and remission or the Lupus Low Disease Activity State in lupus, which the 2023 EULAR lupus recommendations name as treatment targets.27
Insurers and employers tend to add their own questions: how long patients stay on treatment, how much steroid they need, how often they are admitted to hospital and whether they can keep working. These are only answerable when the measures in points 1, 4, 8 and 9 are collected consistently from the start.
What good looks like: outcomes defined against recognised targets before enrolment, measured at consistent intervals, and linked to treatment persistence, steroid use, admissions, infections and patient-reported outcomes.
Matters most to: Pharma programmes, Insurers and employers
Autoimmune data brings together diagnoses, medications, reproductive plans and sometimes mental health, and many patients are understandably cautious about who can see it, particularly where employers or insurers are involved. It falls within the special categories of health data protected under laws such as the General Data Protection Regulation (GDPR), Singapore's Personal Data Protection Act (PDPA) and, where it applies, the Health Insurance Portability and Accountability Act (HIPAA) in the United States.
Portability matters for a reason specific to this area. Many patient support programmes are tied to one brand. When a patient switches to another company's product, they often leave the programme, and their history leaves with them or is lost. Structuring data to interoperability standards such as Fast Healthcare Interoperability Resources (FHIR) makes it possible for that history to follow the patient, with their consent.
What good looks like: granular consent recorded with the data, pseudonymisation for any use beyond direct care, and a record that can be exported in a standard format with its provenance intact.
Matters most to: Pharma programmes, Insurers and employers, Clinics and laboratories
The twelve points apply across autoimmune care, but each condition has its own measures and data. This summary shows the core items most programmes will need for the four conditions most often treated with biologics.
You do not need to solve all twelve at once. The right starting point depends on what your data needs to do.
Teams tend to get the most from these twelve points when they use them as a working tool rather than a reading list.
If you would like support with this, the Health Data Foundations work within Jonda Health Services takes a programme through exactly these questions, from what data you hold and where it sits to what it needs before it can support analytics, AI or evidence generation. Where the goal is to show outcomes, our insight and analytics work helps turn a harmonised dataset into measures and benchmarks your stakeholders can use.
Much of what sits between an autoimmune programme and the evidence it needs is data work. It means bringing together specialist letters, laboratory results, screening reports, treatment records and patient-reported data, making them usable across formats and languages, cleaning them, resolving the many ways the same thing gets captured, reviewing them clinically and mapping them to medical coding standards. This is the work we do every day.
JondaX, our health data transformation engine, turns laboratory reports, clinical documents, medical device readings and wearable data into structured, harmonised data through a single API, with other clinical data types configured to your needs. Every dataset goes through human-in-the-loop review by clinically trained reviewers, so that the burden of checking does not fall on your team. JondaX can be deployed and processed within your country where required, supports pseudonymisation of data for secondary use, and works with your own ontology and code sets. Jonda Health Services supports teams earlier in the journey, from programme design and outcome definitions to deciding what to build yourselves and what to bring in. Jonda Health is ISO 27001 certified, and our platform is designed to comply with HIPAA, GDPR and PDPA.
At a minimum: a validated disease activity measure recorded with its version, a clear flare definition, the full treatment history including biologic and biosimilar switches and the reason for each, screening and vaccination results, monitoring blood tests with their units, patient-reported outcomes on a validated instrument, and infections and other safety events.
The two versions of the 28-joint Disease Activity Score use different inflammatory markers. Research in early rheumatoid arthritis found DAS28-CRP values were consistently lower than DAS28-ESR values, so the two should not be used interchangeably.8 Programmes should record which version was used for every score.
Record each product as a separate treatment episode with its active ingredient, brand, dose, route, start and stop dates, and a structured reason for the change, such as a non-medical switch, loss of response, intolerance, a funding or supply gap, or pregnancy planning.
The 2022 EULAR recommendations advise screening for latent tuberculosis, with interferon-gamma release assays preferred, and defining hepatitis B status before starting treatment.14 EULAR also recommends checking vaccination status, ideally before planned immunosuppression.16
By collecting consistent, dated measures over time that match recognised treatment targets, such as remission or low disease activity, and linking them to treatment persistence, steroid use, hospital admissions, infections and patient-reported outcomes, with consent for the intended reuse.
This guide is for teams designing and running autoimmune programmes and services. It is not clinical advice for individuals.
