Background. Brain atrophy is a hallmark of multiple sclerosis (MS). For clinical translatability and individual-level predictions, brain atrophy needs to be put into context of the broader population, using reference or normative models. Methods. Reference models of MRI-derived brain volumes were established from a large healthy control (HC) multi-cohort dataset (N=63 115, 51% females). The reference models were applied to two independent MS cohorts (N=362, T1w-scans=953, follow-up time up to 12 years) to assess deviations from the reference, defined as Z-values. We assessed the overlap of deviation profiles and their stability over time using individual-level transitions towards or out of significant reference deviation states (|Z|>1.96). A negative binomial model was used for case-control comparisons of the number of extreme deviations. Linear models were used to assess differences in Z-score deviations between MS and propensity-matched HCs, and associations with clinical scores at baseline and over time. The utilized normative BrainReference models, scripts and usage instructions are freely available. Findings. We identified a temporally stable, brain morphometric phenotype of MS. The right and left thalami most consistently showed significantly lower-than-reference volumes in MS (25% and 26% overlap across the sample). The number of such extreme smaller-than-reference values was 2.70 in MS compared to HC (4.51 versus 1.67). Additional deviations indicated stronger disability (Expanded Disability Status Scale: β=0.22, 95% CI 0.12 to 0.32), Paced Auditory Serial Addition Test score (β=-0.27, 95% CI -0.52 to -0.02), and Fatigue Severity Score (β=0.29, 95% CI 0.05 to 0.53) at baseline, and over time with EDSS (β=0.07, 95% CI 0.02 to 0.13). We additionally provide detailed maps of reference-deviations and their associations with clinical assessments. Interpretation. We present a heterogenous brain phenotype of MS which is associated with clinical manifestations, and particularly implicating the thalamus. The findings offer potential to aid diagnosis and prognosis of MS.

OAA has received a speaker's honorarium from Lundbeck, Janssen, Otsuka and Lilly, and is a consultant to Coretechs.ai and Precision Health. LTW is a minor shareholder of baba.vision. KMM has served on scientific advisory board for Alexion, received speaker honoraria from Biogen, Lundbeck, Novartis and Roche, and has participated in clinical trials organized by Biogen, Merck, Novartis, Otivio, Roche and Sanofi. EAH received honoraria for advisory board activity from Sanofi-Genzyme, and his department has received honoraria for lecturing from Biogen and Merck. OT received speaker honoraria from and served on scientific advisory boards of Biogen, Sanofi-Aventis, Merck, and Novartis, and has participated in clinical trials organized by Merck, Novartis, Roche and Sanofi. SW received speaker honoraria from Biogen, Sanofi-Aventis, and Janssen, and has participated in commissioned research projects funded by Merck, Novartis, and EMD Serono. The remaining authors declare no other competing interests.

https://clinicaltrials.gov/study/NCT00360906

Norwegian MS-union, Research Council of Norway (#223273; #324252); the South-Eastern Norway Regional Health Authority (#2022080); and the European Union's Horizon2020 Research and Innovation Programme (#847776, #802998).

I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

Yes

The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

The study was approved by the Norwegian Regional Committees for Medical and Health Research Ethics (REK-814351, REK-2016/1906) and registered as clinical trial (clinicaltrials.gov identifier: NCT00360906). Healthy control subject data access was obtained under REK 567301, PVO 17/21624.

I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.

Yes

I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).

Yes

I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.

Yes

Summary statistics and utilized code can be found in the GitHub repository: https://github.com/MaxKorbmacher/NormativeModelsMS. Multiple of the utilized dataset are sensitive, require IRB approval for usage, and can therefore not be openly shared.

https://github.com/MaxKorbmacher/NormativeModelsMS