Markov modeling for cost-effectiveness using federated health data network.

OBJECTIVE: To introduce 2 R-packages that facilitate conducting health economics research on OMOP-based data networks, aiming to standardize and improve the reproducibility, transparency, and transferability of health economic models. MATERIALS AND METHODS: We developed the software tools and demonstrated their utility by replicating a UK-based heart failure data analysis across 5 different international databases from Estonia, Spain, Serbia, and the United States. RESULTS: We examined treatment trajectories of 47 163 patients. The overall incremental cost-effectiveness ratio (ICER) for telemonitoring relative to standard of care was 57 472 €/QALY. Country-specific ICERs were 60 312 €/QALY in Estonia, 58 096 €/QALY in Spain, 40 372 €/QALY in Serbia, and 90 893 €/QALY in the US, which surpassed the established willingness-to-pay thresholds. DISCUSSION: Currently, the cost-effectiveness analysis lacks standard tools, is performed in ad-hoc manner, and relies heavily on published information that might not be specific for local circumstances. Published results often exhibit a narrow focus, central to a single site, and provide only partial decision criteria, limiting their generalizability and comprehensive utility. CONCLUSION: We created 2 R-packages to pioneer cost-effectiveness analysis in OMOP CDM data networks. The first manages state definitions and database interaction, while the second focuses on Markov model learning and profile synthesis. We demonstrated their utility in a multisite heart failure study, comparing telemonitoring and standard care, finding telemonitoring not cost-effective.

Transforming Estonian health data to the Observational Medical Outcomes Partnership (OMOP) Common Data Model: lessons learned.

Objective: To describe the reusable transformation process of electronic health records (EHR), claims, and prescriptions data into Observational Medical Outcome Partnership (OMOP) Common Data Model (CDM), together with challenges faced and solutions implemented. Materials and Methods: We used Estonian national health databases that store almost all residents' claims, prescriptions, and EHR records. To develop and demonstrate the transformation process of Estonian health data to OMOP CDM, we used a 10% random sample of the Estonian population (n = 150 824 patients) from 2012 to 2019 (MAITT dataset). For the sample, complete information from all 3 databases was converted to OMOP CDM version 5.3. The validation was performed using open-source tools. Results: In total, we transformed over 100 million entries to standard concepts using standard OMOP vocabularies with the average mapping rate 95%. For conditions, observations, drugs, and measurements, the mapping rate was over 90%. In most cases, SNOMED Clinical Terms were used as the target vocabulary. Discussion: During the transformation process, we encountered several challenges, which are described in detail with concrete examples and solutions. Conclusion: For a representative 10% random sample, we successfully transferred complete records from 3 national health databases to OMOP CDM and created a reusable transformation process. Our work helps future researchers to transform linked databases into OMOP CDM more efficiently, ultimately leading to better real-world evidence.

g:Profiler-interoperable web service for functional enrichment analysis and gene identifier mapping (2023 update).

g:Profiler is a reliable and up-to-date functional enrichment analysis tool that supports various evidence types, identifier types and organisms. The toolset integrates many databases, including Gene Ontology, KEGG and TRANSFAC, to provide a comprehensive and in-depth analysis of gene lists. It also provides interactive and intuitive user interfaces and supports ordered queries and custom statistical backgrounds, among other settings. g:Profiler provides multiple programmatic interfaces to access its functionality. These can be easily integrated into custom workflows and external tools, making them valuable resources for researchers who want to develop their own solutions. g:Profiler has been available since 2007 and is used to analyse millions of queries. Research reproducibility and transparency are achieved by maintaining working versions of all past database releases since 2015. g:Profiler supports 849 species, including vertebrates, plants, fungi, insects and parasites, and can analyse any organism through user-uploaded custom annotation files. In this update article, we introduce a novel filtering method highlighting Gene Ontology driver terms, accompanied by new graph visualizations providing a broader context for significant Gene Ontology terms. As a leading enrichment analysis and gene list interoperability service, g:Profiler offers a valuable resource for genetics, biology and medical researchers. It is freely accessible at https://biit.cs.ut.ee/gprofiler.

Common clinical blood and urine biomarkers for ischemic stroke: an Estonian Electronic Health Records database study.

BACKGROUND: Ischemic stroke (IS) is a major health risk without generally usable effective measures of primary prevention. Early warning signals that are easy to detect and widely available can save lives. Estonia has one nation-wide Electronic Health Record (EHR) database for the storage of medical information of patients from hospitals and primary care providers. METHODS: We extracted structured and unstructured data from the EHRs of participants of the Estonian Biobank (EstBB) and evaluated different formats of input data to understand how this continuously growing dataset should be prepared for best prediction. The utility of the EHR database for finding blood- and urine-based biomarkers for IS was demonstrated by applying different analytical and machine learning (ML) methods. RESULTS: Several early trends in common clinical laboratory parameter changes (set of red blood indices, lymphocyte/neutrophil ratio, etc.) were established for IS prediction. The developed ML models predicted the future occurrence of IS with very high accuracy and Random Forests was proved as the most applicable method to EHR data. CONCLUSIONS: We conclude that the EHR database and the risk factors uncovered are valuable resources in screening the population for risk of IS as well as constructing disease risk scores and refining prediction models for IS by ML.

Prevaccination Prevalence of Type-Specific Human Papillomavirus Infection by Grade of Cervical Cytology in Estonia.

Importance: Large-scale data on type-specific human papillomavirus (HPV) prevalence and disease burden worldwide are needed to guide cervical cancer prevention efforts. Promoting the research and application of health care big data has become a key factor in modern medical research. Objective: To examine the prevaccination prevalence of high-risk HPV (hrHPV) and type distribution by cervical cytology grade in Estonia. Design, Setting, and Participants: This cross-sectional study used text mining and the linking of data from electronic health records and health care claims to examine type-specific hrHPV positivity in Estonia from 2012 to 2019. Participants were women aged at least 18 years. Statistical analysis was performed from September 2021 to August 2022. Main Outcomes and Measures: Type-specific hrHPV positivity rate by cervical cytological grade. Results: A total of 11 017 cases of cervical cytology complemented with data on hrHPV testing results between 2012 and 2019 from 66 451 women aged at least 18 years (mean [SD] age, 48.1 [21.0] years) were included. The most common hrHPV types were HPV16, 18, 31, 33, 51 and 52, which accounted for 73.8% of all hrHPV types detected. There was a marked decline in the positivity rate of hrHPV infection with increasing age, but the proportion did not vary significantly based on HPV type. Implementation of nonavalent prophylactic vaccination was estimated to reduce the number of women with high-grade cytology by 50.5% (95% CI, 47.4%-53.6%) and the number with low-grade cytology by 27.8% (95% CI, 26.3%-29.3%), giving an overall estimated reduction of 33.1% (95% CI, 31.7%-34.5%) in the number of women with precancerous cervical cytology findings. Conclusions and Relevance: In this cross-sectional study, text mining and natural language processing techniques allowed the detection of precursors to cervical cancer based on data stored by the nationwide health system. These findings contribute to the literature on type-specific HPV distribution by cervical cytology grade and document that α-9 phylogenetic group HPV types 16, 31, 33, 52 and α-7 phylogenetic group HPV 18 are the most frequently detected in normal-to-high-grade precancerous lesions in Estonia.

Omics-informed CNV calls reduce false-positive rates and improve power for CNV-trait associations.

Copy-number variations (CNV) are believed to play an important role in a wide range of complex traits, but discovering such associations remains challenging. While whole-genome sequencing (WGS) is the gold-standard approach for CNV detection, there are several orders of magnitude more samples with available genotyping microarray data. Such array data can be exploited for CNV detection using dedicated software (e.g., PennCNV); however, these calls suffer from elevated false-positive and -negative rates. In this study, we developed a CNV quality score that weights PennCNV calls (pCNVs) based on their likelihood of being true positive. First, we established a measure of pCNV reliability by leveraging evidence from multiple omics data (WGS, transcriptomics, and methylomics) obtained from the same samples. Next, we built a predictor of omics-confirmed pCNVs, termed omics-informed quality score (OQS), using only PennCNV software output parameters. Promisingly, OQS assigned to pCNVs detected in close family members was up to 35% higher than the OQS of pCNVs not carried by other relatives (p < 3.0 × 10-90), outperforming other scores. Finally, in an association study of four anthropometric traits in 89,516 Estonian Biobank samples, the use of OQS led to a relative increase in the trait variance explained by CNVs of up to 56% compared with published quality filtering methods or scores. Overall, we put forward a flexible framework to improve any CNV detection method leveraging multi-omics evidence, applied it to improve PennCNV calls, and demonstrated its utility by improving the statistical power for downstream association analyses.

Functional Annotation of Custom Transcriptomes.

Many eukaryotic genes can give rise to different alternative transcripts depending on stage of development, cell type, and physiological cues. Current transcriptome-wide sequencing technologies highlight the remarkable extent of this regulation in metazoans and allow for RNA isoforms to be profiled in increasingly small biological samples and with a growing confidence. Understanding biological functions of sample-specific transcripts is a major challenge in genomics and RNA processing fields. Here we describe simple bioinformatics workflows that facilitate this task by streamlining reference-guided annotation of novel transcripts. A key part of our protocol is the R package factR that rapidly matches custom-assembled transcripts to their likely host genes, deduces the sequence and domain structure of novel protein products, and predicts sensitivity of newly identified RNA isoforms to nonsense-mediated decay.

Trajectories: a framework for detecting temporal clinical event sequences from health data standardized to the Observational Medical Outcomes Partnership (OMOP) Common Data Model.

Objective: To develop a framework for identifying temporal clinical event trajectories from Observational Medical Outcomes Partnership-formatted observational healthcare data. Materials and Methods: A 4-step framework based on significant temporal event pair detection is described and implemented as an open-source R package. It is used on a population-based Estonian dataset to first replicate a large Danish population-based study and second, to conduct a disease trajectory detection study for type 2 diabetes patients in the Estonian and Dutch databases as an example. Results: As a proof of concept, we apply the methods in the Estonian database and provide a detailed breakdown of our findings. All Estonian population-based event pairs are shown. We compare the event pairs identified from Estonia to Danish and Dutch data and discuss the causes of the differences. The overlap in the results was only 2.4%, which highlights the need for running similar studies in different populations. Conclusions: For the first time, there is a complete software package for detecting disease trajectories in health data.

PAWER: protein array web exploreR.

BACKGROUND: Protein microarray is a well-established approach for characterizing activity levels of thousands of proteins in a parallel manner. Analysis of protein microarray data is complex and time-consuming, while existing solutions are either outdated or challenging to use without programming skills. The typical data analysis pipeline consists of a data preprocessing step, followed by differential expression analysis, which is then put into context via functional enrichment. Normally, biologists would need to assemble their own workflow by combining a set of unrelated tools to analyze experimental data. Provided that most of these tools are developed independently by various bioinformatics groups, making them work together could be a real challenge. RESULTS: Here we present PAWER, the online web tool dedicated solely to protein microarray analysis. PAWER enables biologists to carry out all the necessary analysis steps in one go. PAWER provides access to state-of-the-art computational methods through the user-friendly interface, resulting in publication-ready illustrations. We also provide an R package for more advanced use cases, such as bespoke analysis workflows. CONCLUSIONS: PAWER is freely available at https://biit.cs.ut.ee/pawer .

Healthspan pathway maps in C. elegans and humans highlight transcription, proliferation/biosynthesis and lipids.

The molecular basis of aging and of aging-associated diseases is being unraveled at an increasing pace. An extended healthspan, and not merely an extension of lifespan, has become the aim of medical practice. Here, we define health based on the absence of diseases and dysfunctions. Based on an extensive review of the literature, in particular for humans and C. elegans, we compile a list of features of health and of the genes associated with them. These genes may or may not be associated with survival/lifespan. In turn, survival/lifespan genes that are not known to be directly associated with health are not considered. Clusters of these genes based on molecular interaction data give rise to maps of healthspan pathways for humans and for C. elegans. Overlaying healthspan-related gene expression data onto the healthspan pathway maps, we observe the downregulation of (pro-inflammatory) Notch signaling in humans and of proliferation in C. elegans. We identify transcription, proliferation/biosynthesis and lipids as a common theme on the annotation level, and proliferation-related kinases on the gene/protein level. Our literature-based data corpus, including visualization, should be seen as a pilot investigation of the molecular underpinnings of health in two different species. Web address: http://pathways.h2020awe.eu.

gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler.

g:Profiler ( https://biit.cs.ut.ee/gprofiler) is a widely used gene list functional profiling and namespace conversion toolset that has been contributing to reproducible biological data analysis already since 2007. Here we introduce the accompanying R package, gprofiler2, developed to facilitate programmatic access to g:Profiler computations and databases via REST API. The gprofiler2 package provides an easy-to-use functionality that enables researchers to incorporate functional enrichment analysis into automated analysis pipelines written in R. The package also implements interactive visualisation methods to help to interpret the enrichment results and to illustrate them for publications. In addition, gprofiler2 gives access to the versatile gene/protein identifier conversion functionality in g:Profiler enabling to map between hundreds of different identifier types or orthologous species. The gprofiler2 package is freely available at the CRAN repository.

HENA, heterogeneous network-based data set for Alzheimer's disease.

Alzheimer's disease and other types of dementia are the top cause for disabilities in later life and various types of experiments have been performed to understand the underlying mechanisms of the disease with the aim of coming up with potential drug targets. These experiments have been carried out by scientists working in different domains such as proteomics, molecular biology, clinical diagnostics and genomics. The results of such experiments are stored in the databases designed for collecting data of similar types. However, in order to get a systematic view of the disease from these independent but complementary data sets, it is necessary to combine them. In this study we describe a heterogeneous network-based data set for Alzheimer's disease (HENA). Additionally, we demonstrate the application of state-of-the-art graph convolutional networks, i.e. deep learning methods for the analysis of such large heterogeneous biological data sets. We expect HENA to allow scientists to explore and analyze their own results in the broader context of Alzheimer's disease research.

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update).

Biological data analysis often deals with lists of genes arising from various studies. The g:Profiler toolset is widely used for finding biological categories enriched in gene lists, conversions between gene identifiers and mappings to their orthologs. The mission of g:Profiler is to provide a reliable service based on up-to-date high quality data in a convenient manner across many evidence types, identifier spaces and organisms. g:Profiler relies on Ensembl as a primary data source and follows their quarterly release cycle while updating the other data sources simultaneously. The current update provides a better user experience due to a modern responsive web interface, standardised API and libraries. The results are delivered through an interactive and configurable web design. Results can be downloaded as publication ready visualisations or delimited text files. In the current update we have extended the support to 467 species and strains, including vertebrates, plants, fungi, insects and parasites. By supporting user uploaded custom GMT files, g:Profiler is now capable of analysing data from any organism. All past releases are maintained for reproducibility and transparency. The 2019 update introduces an extensive technical rewrite making the services faster and more flexible. g:Profiler is freely available at https://biit.cs.ut.ee/gprofiler.

An exploratory phenome wide association study linking asthma and liver disease genetic variants to electronic health records from the Estonian Biobank.

The Estonian Biobank, governed by the Institute of Genomics at the University of Tartu (Biobank), has stored genetic material/DNA and continuously collected data since 2002 on a total of 52,274 individuals representing ~5% of the Estonian adult population and is increasing. To explore the utility of data available in the Biobank, we conducted a phenome-wide association study (PheWAS) in two areas of interest to healthcare researchers; asthma and liver disease. We used 11 asthma and 13 liver disease-associated single nucleotide polymorphisms (SNPs), identified from published genome-wide association studies, to test our ability to detect established associations. We confirmed 2 asthma and 5 liver disease associated variants at nominal significance and directionally consistent with published results. We found 2 associations that were opposite to what was published before (rs4374383:AA increases risk of NASH/NAFLD, rs11597086 increases ALT level). Three SNP-diagnosis pairs passed the phenome-wide significance threshold: rs9273349 and E06 (thyroiditis, p = 5.50x10-8); rs9273349 and E10 (type-1 diabetes, p = 2.60x10-7); and rs2281135 and K76 (non-alcoholic liver diseases, including NAFLD, p = 4.10x10-7). We have validated our approach and confirmed the quality of the data for these conditions. Importantly, we demonstrate that the extensive amount of genetic and medical information from the Estonian Biobank can be successfully utilized for scientific research.

Comparison of variation in frequency for SNPs associated with asthma or liver disease between Estonia, HapMap populations and the 1000 genome project populations.

Allele-specific analyses to understand frequency differences across populations, particularly populations not well studied, are important to help identify variants that may have a functional effect on disease mechanisms and phenotypic predisposition, facilitating new Genome-Wide Association Studies (GWAS). We aimed to compare the allele frequency of 11 asthma-associated and 16 liver disease-associated single nucleotide polymorphisms (SNPs) between the Estonian, HapMap and 1000 genome project populations. When comparing EGCUT with HapMap populations, the largest difference in allele frequencies was observed with the Maasai population in Kinyawa, Kenya, with 12 SNP variants reporting statistical significance. Similarly, when comparing EGCUT with 1000 genomes project populations, the largest difference in allele frequencies was observed with pooled African populations with 22 SNP variants reporting statistical significance. For 11 asthma-associated and 16 liver disease-associated SNPs, Estonians are genetically similar to other European populations but significantly different from African populations. Understanding differences in genetic architecture between ethnic populations is important to facilitate new GWAS targeted at underserved ethnic groups to enable novel genetic findings to aid the development of new therapies to reduce morbidity and mortality.

Genetic variation in the Estonian population: pharmacogenomics study of adverse drug effects using electronic health records.

Pharmacogenomics aims to tailor pharmacological treatment to each individual by considering associations between genetic polymorphisms and adverse drug effects (ADEs). With technological advances, pharmacogenomic research has evolved from candidate gene analyses to genome-wide association studies. Here, we integrate deep whole-genome sequencing (WGS) information with drug prescription and ADE data from Estonian electronic health record (EHR) databases to evaluate genome- and pharmacome-wide associations on an unprecedented scale. We leveraged WGS data of 2240 Estonian Biobank participants and imputed all single-nucleotide variants (SNVs) with allele counts over 2 for 13,986 genotyped participants. Overall, we identified 41 (10 novel) loss-of-function and 567 (134 novel) missense variants in 64 very important pharmacogenes. The majority of the detected variants were very rare with frequencies below 0.05%, and 6 of the novel loss-of-function and 99 of the missense variants were only detected as single alleles (allele count = 1). We also validated documented pharmacogenetic associations and detected new independent variants in known gene-drug pairs. Specifically, we found that CTNNA3 was associated with myositis and myopathies among individuals taking nonsteroidal anti-inflammatory oxicams and replicated this finding in an extended cohort of 706 individuals. These findings illustrate that population-based WGS-coupled EHRs are a useful tool for biomarker discovery.

Translating genotype data of 44,000 biobank participants into clinical pharmacogenetic recommendations: challenges and solutions.

PURPOSE: Biomedical databases combining electronic medical records and phenotypic and genomic data constitute a powerful resource for the personalization of treatment. To leverage the wealth of information provided, algorithms are required that systematically translate the contained information into treatment recommendations based on existing genotype-phenotype associations. METHODS: We developed and tested algorithms for translation of preexisting genotype data of over 44,000 participants of the Estonian biobank into pharmacogenetic recommendations. We compared the results obtained by genome sequencing, exome sequencing, and genotyping using microarrays, and evaluated the impact of pharmacogenetic reporting based on drug prescription statistics in the Nordic countries and Estonia. RESULTS: Our most striking result was that the performance of genotyping arrays is similar to that of genome sequencing, whereas exome sequencing is not suitable for pharmacogenetic predictions. Interestingly, 99.8% of all assessed individuals had a genotype associated with increased risks to at least one medication, and thereby the implementation of pharmacogenetic recommendations based on genotyping affects at least 50 daily drug doses per 1000 inhabitants. CONCLUSION: We find that microarrays are a cost-effective solution for creating preemptive pharmacogenetic reports, and with slight modifications, existing databases can be applied for automated pharmacogenetic decision support for clinicians.

funcExplorer: a tool for fast data-driven functional characterisation of high-throughput expression data.

BACKGROUND: A widely applied approach to extract knowledge from high-throughput genomic data is clustering of gene expression profiles followed by functional enrichment analysis. This type of analysis, when done manually, is highly subjective and has limited reproducibility. Moreover, this pipeline can be very time-consuming and resource-demanding as enrichment analysis is done for tens to hundreds of clusters at a time. Thus, the task often needs programming skills to form a pipeline of different software tools or R packages to enable an automated approach. Furthermore, visualising the results can be challenging. RESULTS: We developed a web tool, funcExplorer, which automatically combines hierarchical clustering and enrichment analysis to detect functionally related gene clusters. The functional characterisation is achieved using structured knowledge from data sources such as Gene Ontology, KEGG and Reactome pathways, Human Protein Atlas, and Human Phenotype Ontology. funcExplorer includes various measures for finding biologically meaningful clusters, provides a modern graphical user interface, and has wide-ranging data export and sharing options as well as software transparency by open-source code. The results are presented in a visually compact and interactive format, enabling users to explore the biological essence of the data. We compared our results with previously published gene clusters to demonstrate that funcExplorer can perform the data characterisation equally well, but without requiring labour-intensive manual interference. CONCLUSIONS: The open-source web tool funcExplorer enables scientists with high-throughput genomic data to obtain a preliminary interactive overview of the expression patterns, gene names, and shared functionalities in their dataset in a visually pleasing format. funcExplorer is publicly available at https://biit.cs.ut.ee/funcexplorer.

Validating Fitbit Zip for monitoring physical activity of children in school: a cross-sectional study.

BACKGROUND: Modern activity trackers, including the Fitbit Zip, enable the measurement of both the step count as well as physical activity (PA) intensities. However, there is a need for field-based validation studies in a variety of populations before using trackers for research. Therefore, the purpose of the current study was to investigate the validity of Fitbit Zip step count, moderate to vigorous physical activity (MVPA) and sedentary minutes, in different school segments in 3rd grade students. METHODS: Third grade students (N = 147, aged 9-10 years) wore a Fitbit Zip and an ActiGraph GT3x-BT accelerometer simultaneously on a belt for five days during school hours. The number of steps, minutes of MVPA and sedentary time during class time, physical education lessons and recess were extracted from both devices using time filters, based on the information from school time tables obtained from class teachers. The validity of the Fitbit Zip in different school segments was assessed using Bland-Altman analysis and Spearman's correlation. RESULTS: There was a strong correlation in the number of steps in all in-school segments between the two devices (r = 0.85-0.96, P < 0.001). The Fitbit Zip overestimated the number of steps in all segments, with the greatest overestimation being present in physical education lessons (345 steps). As for PA intensities, the agreement between the two devices in physical education and recess was moderate for MVPA minutes (r = 0.56 and r = 0.72, P < 0.001, respectively) and strong for sedentary time (r = 0.85 and r = 0.87, P < 0.001, respectively). During class time, the correlation was weak for MVPA minutes (r = 0.24, P < 0.001) and moderate for sedentary time (r = 0.57, P < 0.001). For total in-school time, the correlation between the two devices was strong for steps (r = 0.98, P < 0.001), MVPA (r = 0.80, P < 0.001) and sedentary time (r = 0.94, P < 0.001). CONCLUSION: In general, the Fitbit Zip can be considered a relatively accurate device for measuring the number of steps, MVPA and sedentary time in students in a school-setting. However, in segments where sedentary time dominates (e.g. academic classes), a research-grade accelerometer should be preferred.

Prostaglandin D2 Receptor DP1 Antibodies Predict Vaccine-induced and Spontaneous Narcolepsy Type 1: Large-scale Study of Antibody Profiling.

BACKGROUND: Neuropathological findings support an autoimmune etiology as an underlying factor for loss of orexin-producing neurons in spontaneous narcolepsy type 1 (narcolepsy with cataplexy; sNT1) as well as in Pandemrix influenza vaccine-induced narcolepsy type 1 (Pdmx-NT1). The precise molecular target or antigens for the immune response have, however, remained elusive. METHODS: Here we have performed a comprehensive antigenic repertoire analysis of sera using the next-generation phage display method - mimotope variation analysis (MVA). Samples from 64 children and adolescents were analyzed: 10 with Pdmx-NT1, 6 with sNT1, 16 Pandemrix-vaccinated, 16 H1N1 infected, and 16 unvaccinated healthy individuals. The diagnosis of NT1 was defined by the American Academy of Sleep Medicine international criteria of sleep disorders v3. FINDINGS: Our data showed that although the immunoprofiles toward vaccination were generally similar in study groups, there were also striking differences in immunoprofiles between sNT1 and Pdmx-NT1 groups as compared with controls. Prominent immune response was observed to a peptide epitope derived from prostaglandin D2 receptor (DP1), as well as peptides homologous to B cell lymphoma 6 protein. Further validation confirmed that these can act as true antigenic targets in discriminating NT1 diseased along with a novel epitope of hemagglutinin of H1N1 to delineate exposure to H1N1. INTERPRETATION: We propose that DP1 is a novel molecular target of autoimmune response and presents a potential diagnostic biomarker for NT1. DP1 is involved in the regulation of non-rapid eye movement (NREM) sleep and thus alterations in its functions could contribute to the disturbed sleep regulation in NT1 that warrants further studies. Together our results also show that MVA is a helpful method for finding novel peptide antigens to classify human autoimmune diseases, possibly facilitating the design of better therapies.