Dataset Information

A scoping review and proposed workflow for multi-omic rare disease research.

ABSTRACT: BACKGROUND:Patients with rare diseases face unique challenges in obtaining a diagnosis, appropriate medical care and access to support services. Whole genome and exome sequencing have increased identification of causal variants compared to single gene testing alone, with diagnostic rates of approximately 50% for inherited diseases, however integrated multi-omic analysis may further increase diagnostic yield. Additionally, multi-omic analysis can aid the explanation of genotypic and phenotypic heterogeneity, which may not be evident from single omic analyses. MAIN BODY:This scoping review took a systematic approach to comprehensively search the electronic databases MEDLINE, EMBASE, PubMed, Web of Science, Scopus, Google Scholar, and the grey literature databases OpenGrey / GreyLit for journal articles pertaining to multi-omics and rare disease, written in English and published prior to the 30th December 2018. Additionally, The Cancer Genome Atlas publications were searched for relevant studies and forward citation searching / screening of reference lists was performed to identify further eligible articles. Following title, abstract and full text screening, 66 articles were found to be eligible for inclusion in this review. Of these 42 (64%) were studies of multi-omics and rare cancer, two (3%) were studies of multi-omics and a pre-cancerous condition, and 22 (33.3%) were studies of non-cancerous rare diseases. The average age of participants (where known) across studies was 39.4?years. There has been a significant increase in the number of multi-omic studies in recent years, with 66.7% of included studies conducted since 2016 and 33% since 2018. Fourteen combinations of multi-omic analyses for rare disease research were returned spanning genomics, epigenomics, transcriptomics, proteomics, phenomics and metabolomics. CONCLUSIONS:This scoping review emphasises the value of multi-omic analysis for rare disease research in several ways compared to single omic analysis, ranging from the provision of a diagnosis, identification of prognostic biomarkers, distinct molecular subtypes (particularly for rare cancers), and identification of novel therapeutic targets. Moving forward there is a critical need for collaboration of multi-omic rare disease studies to increase the potential to generate robust outcomes and development of standardised biorepository collection and reporting structures for multi-omic studies.

SUBMITTER: Kerr K

PROVIDER: S-EPMC7189570 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A scoping review and proposed workflow for multi-omic rare disease research.

Kerr Katie K McAneney Helen H Smyth Laura J LJ Bailie Caitlin C McKee Shane S McKnight Amy Jayne AJ

Orphanet journal of rare diseases 20200428 1

<h4>Background</h4>Patients with rare diseases face unique challenges in obtaining a diagnosis, appropriate medical care and access to support services. Whole genome and exome sequencing have increased identification of causal variants compared to single gene testing alone, with diagnostic rates of approximately 50% for inherited diseases, however integrated multi-omic analysis may further increase diagnostic yield. Additionally, multi-omic analysis can aid the explanation of genotypic and pheno ...[more]

PMID: 32345347

Similar Datasets

Project description:To better understand dynamic disease processes, integrated multi-omic methods are needed, yet comparing different types of omic data remains difficult. Integrative solutions benefit experimenters by eliminating potential biases that come with single omic analysis. We have developed the methods needed to explore whether a relationship exists between co-expression network models built from transcriptomic and proteomic data types, and whether this relationship can be used to improve the disease signature discovery process. A naïve, correlation based method is utilized for comparison. Using publicly available infectious disease time series data, we analyzed the related co-expression structure of the transcriptome and proteome in response to SARS-CoV infection in mice. Transcript and peptide expression data was filtered using quality scores and subset by taking the intersection on mapped Entrez IDs. Using this data set, independent co-expression networks were built. The networks were integrated by constructing a bipartite module graph based on module member overlap, module summary correlation, and correlation to phenotypes of interest. Compared to the module level results, the naïve approach is hindered by a lack of correlation across data types, less significant enrichment results, and little functional overlap across data types. Our module graph approach avoids these problems, resulting in an integrated omic signature of disease progression, which allows prioritization across data types for down-stream experiment planning. Integrated modules exhibited related functional enrichments and could suggest novel interactions in response to infection. These disease and platform-independent methods can be used to realize the full potential of multi-omic network signatures. The data (experiment SM001) are publically available through the NIAID Systems Virology (https://www.systemsvirology.org) and PNNL (http://omics.pnl.gov) web portals. Phenotype data is found in the supplementary information. The ProCoNA package is available as part of Bioconductor 2.13.

Project description:Background: Research on disparities in traumatic injury has not been well characterized, limiting understanding of gaps in research and development of successful interventions. We conducted a scoping review to identify and synthesize research on disparities in intentional and unintentional traumatic injuries. Methods: The review was guided by PRISMA Extension for Scoping Reviews. PubMed, PsycINFO, Web of Science, and CINAHL and systematic reviews from 2007 to 2017 were searched. Eligible articles were peer reviewed; conducted in the United States; and reported on clearly defined physical trauma and disparity, defined by Cochrane PROGRESS-Plus criteria. One reviewer assessed article titles and a second reviewer validated the inclusion with a random sample. Abstract and full-text review by two reviewers determined final inclusion. Results: Of 7382 unique articles screened, 653 articles were included; inter-rater agreement was high (K=0.995). Studies reported on disparities in the acute hospital setting (104) or postacute/rehabilitation (86), with fewer focused on prevention (57) and policy development (6). Research methods used were quantitative (593) with 25 intervention studies, qualitative (45), qualitative/quantitative (7), and community-based participatory research (8). Age ranges of included studies were all ages (124), adults (318), pediatric/youth/adolescents (172), and older adults (40). Racial disparities were most commonly measured (439 studies); 38 created a white/nonwhite binary. Other commonly measured disparities were place of residence (122), insurance (111 studies), gender (89), age (75), and socioeconomic status measures (61). Disparities were noted in all of the categories. Studies commonly aggregated all types of traumatic injuries (129) or all types of violence (105). Conclusions: The extant injury literature lacks research on prevention and policy to address disparities. Many studies aggregated types of trauma and patient groups, preventing an understanding of distinctions between groups and potential interventions. Intervention and community-based research strategies were limited. Future research can better specify measurement of understudied equity categories, trauma types and intent, and racial groups.

Project description:BackgroundExperienced fatigue is an under-recognized and under-researched feature in persons with many different rare diseases. A better overview of the characteristics of existing research on experienced fatigue in children and adults with rare diseases is needed. The purpose of this review was to map and describe characteristics of existing research on experienced fatigue in a selection of rare diseases in rare developmental defects or anomalies during embryogenesis and rare genetic diseases. Furthermore, to identify research gaps and point to research agendas.MethodsWe applied a scoping review methodology, and performed a systematic search in March 2020 in bibliographic databases. References were sorted and evaluated for inclusion using EndNote and Rayyan. Data were extracted on the main research questions concerning characteristics of research on experienced fatigue (definition and focus on fatigue, study populations, research questions investigated and methods used).ResultsThis review included 215 articles on ten different rare developmental defects/anomalies during embryogenesis and 35 rare genetic diseases. Of the 215 articles, 82 had investigation of experienced fatigue as primary aim or outcome. Included were 9 secondary research articles (reviews) and 206 primary research articles. A minority of articles included children. There were large differences in the number of studies in different diseases. Only 29 of 215 articles gave a description of how they defined the concept of experienced fatigue. The most common research-question reported on was prevalence and/ -or associations to fatigue. The least common was diagnostics (development or validation of fatigue assessment methods for a specific patient group). A large variety of methods were used to investigate experienced fatigue, impeding comparisons both within and across diagnoses.ConclusionThis scoping review on the characteristics of fatigue research in rare diseases found a large variety of research on experienced fatigue. However, the minority of studies had investigation of experienced fatigue as a primary aim. There was large variation in how experienced fatigue was defined and also in how it was measured, both within and across diagnoses. More research on experienced fatigue is needed, both in children and adults with rare diseases. This review offers a basis for further research.

Dataset Information

A scoping review and proposed workflow for multi-omic rare disease research.

Publications

A scoping review and proposed workflow for multi-omic rare disease research.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets