BACKGROUND: Multi-organ autoimmunity belongs to a group of ultrarare diseases characterized by complex autoimmune or autoinflammatory processes affecting multiple organs. In addition to adequate medical care for patients with multi-organ autoimmunity, the understanding of patients' treatment preferences and the measurement of their health-related quality of life are essential for improving therapy for these patients.

OBJECTIVE: This study has three goals: (1) to compile a modular questionnaire package using established instruments to assess health-related quality of life and health status; (2) to develop, through a participatory process, and conduct psychometric testing of a new self-report questionnaire assessing patients' treatment preferences; and (3) to evaluate quality of life and patients' preferences in a longitudinal study.

METHODS: To address our goals, we are conducting a mixed methods study involving 300 adult patients undergoing treatment for multi-organ autoimmune diseases; the study includes qualitative interviews with patients and their physicians and a quantitative longitudinal study with 4 measurement time points (at study enrollment and at 3, 6, and 9 months later). We will address our first goal by conducting psychometric analyses to assess the applicability of the modularized questionnaire package to our target population. We will determine item characteristics and conduct exploratory factor analyses and internal consistency analyses with the scales used to assess generic and disease-specific quality of life, as well as disease-specific health status. To address our second goal, we will conduct (1) qualitative interviews with patients and their physicians to explore the preferences of our target population, (2) a 2-round Delphi study to select preferences that are highly relevant to most patients, (3) cognitive pretests to ensure the acceptability and comprehensibility of the scale items and instructions, and (4) psychometric analyses to guide item selection and evaluate the reliability and validity of the final scales.

RESULTS: This paper describes the protocol for the longitudinal cohort study of the research project Qualy-GAIN (German Multi-Organ Auto-Immunity Network), which was funded from January 2023 to December 2025. Data were collected at 4 measurement points from July 2024 to June 2025. First results are expected to be submitted for publication in spring 2026.

CONCLUSIONS: A result of this study will be a package of questionnaires that can be used to assess health-related quality of life, disease-specific health status, and treatment preferences. Due to the voluntary nature of participation and the low burden associated with participation, we believe that the benefits of the study outweigh potential risks. In case the questionnaires evaluated in this study prove to be reliable, valid, and useful in practice, they can be transferred to the routine treatment of patients with multi-organ autoimmune diseases to improve treatment and promote patient-centered care.