Standardized metadata collection to reinforce collaboration in Collaborative Research Centers

We present our approach for research (meta)data exchange and interconnection of scientists in medium-scale academic projects such as medical collaborative research centers (CRCs). Our webbased tool, fredato, connects established services, which we configure to a custom-tailored software bundle to match the needs of researchers. To improve collaboration, we implemented a metadata acquisition component and search function to complement the existing data management and sharing. More specifically, we enhance three points: 1. Relevant projects need to be findable to re-use data or results, avoid redundant work and improve communication among crc members. 2. The scientists also process sensitive human data for which a privacy-protected, secure exchange is critical. 3. A self-explanatory user interface is required for increased user acceptance. The main feature we present is the handling of metadata in our web application without overwhelming users through extensive and generic forms. We use flexible JSON schemas to precisely target scientists' needs of documentation and enrich them with only ontology components relevant to their use cases. The schemas are stored distributedly as datasets themselves, and automatically converted to modern web forms. Besides custom, domain-specific forms we use this editor for the addition of common metadata schemas (e.g. DataCite). We use the continuous integration capabilities of a connected Gitlab to run data-driven scripts. This includes indexing of all metadata, which makes them searchable in a structured way. Users are provided with contact information for matches and can ask to share data and results. Because project owners decide with whom to share and because datasets and metadata are bundled together, the complete dataset is always accessible (e.g. for publication at a third party repository) and full control retained by data owners. By adding this component to our tool, we provide simple, secure and searchable means for improving collaboration in the context of CRCs

Netboost: boosting-supported network analysis improves high-dimensional omics prediction in acute myeloid leukemia and Huntington’s disease

State-of-the art selection methods fail to identify weak but cumulative effects of features found in many high-dimensional omics datasets. Nevertheless, these features play an important role in certain diseases. We present Netboost, a three-step dimension reduction technique. First, a boosting-based filter is combined with the topological overlap measure to identify the essential edges of the network. Second, sparse hierarchical clustering is applied on the selected edges to identify modules and finally module information is aggregated by the first principal components. We demonstrate the application of the newly developed Netboost in combination with CoxBoost for survival prediction of DNA methylation and gene expression data from 180 acute myeloid leukemia (AML) patients and show, based on cross-validated prediction error curve estimates, its prediction superiority over variable selection on the full dataset as well as over an alternative clustering approach. The identified signature related to chromatin modifying enzymes was replicated in an independent dataset, the phase II AMLSG 12-09 study. In a second application we combine Netboost with Random Forest classification and improve the disease classification error in RNA-sequencing data of Huntington's disease mice. Netboost is a freely available Bioconductor R package for dimension reduction and hypothesis generation in high-dimensional omics applications

NOX1 loss-of-function genetic variants in patients with inflammatory bowel disease.

Genetic defects that affect intestinal epithelial barrier function can present with very early-onset inflammatory bowel disease (VEOIBD). Using whole-genome sequencing, a novel hemizygous defect in NOX1 encoding NAPDH oxidase 1 was identified in a patient with ulcerative colitis-like VEOIBD. Exome screening of 1,878 pediatric patients identified further seven male inflammatory bowel disease (IBD) patients with rare NOX1 mutations. Loss-of-function was validated in p.N122H and p.T497A, and to a lesser degree in p.Y470H, p.R287Q, p.I67M, p.Q293R as well as the previously described p.P330S, and the common NOX1 SNP p.D360N (rs34688635) variant. The missense mutation p.N122H abrogated reactive oxygen species (ROS) production in cell lines, ex vivo colonic explants, and patient-derived colonic organoid cultures. Within colonic crypts, NOX1 constitutively generates a high level of ROS in the crypt lumen. Analysis of 9,513 controls and 11,140 IBD patients of non-Jewish European ancestry did not reveal an association between p.D360N and IBD. Our data suggest that loss-of-function variants in NOX1 do not cause a Mendelian disorder of high penetrance but are a context-specific modifier. Our results implicate that variants in NOX1 change brush border ROS within colonic crypts at the interface between the epithelium and luminal microbes

Needs assessment towards research data management at the Medical Faculty of the University of Freiburg – Data of the BE-KONFORM study

In order to investigate employees’ needs of the Medical Faculty of the University of Freiburg regarding research data management, the BE-KONFORM study was performed in a two-step approach. First, guideline-based qualitative video interviews with four researchers were performed to identify key constructs of relevance. Second, a standardized online survey was conducted from 1st to 15th of November 2020 based on e-mail invitation by the dean and a faculty newsletter. The questionnaire was provided bilingual (English and German) using a backward-forward translation method, no reminders and incentives were used to increase the response rate. The online survey was programmed in REDCap and was accessible via online link. The target population were members of the Medical Faculty (listed in the newsletter mailing list) regardless of the type of working contract signed. The final dataset contains 236 complete cases (90% German and 10% English). The study includes a randomised module asking for data publication (group A) or not (group B). 113 cases were randomized into group A and 99% of them consented to the publication of the collected research data in anonymized form (n=112). The dataset comprised questions about work-related characteristics (professional status, working experience, scientific field of work), data management-related items (definition of research data management, type of data used, type of storage used for saving data, use of electronic laboratory notebooks), experience and attitudes towards data publication in data repositories, as well as needs and preferences regarding research data management support. The produced data offers the possibility to connect with other data collected in this field in other contexts (faculties or universities)

Homozygous and Compound-Heterozygous Mutations in TGDS Cause Catel-Manzke Syndrome

Catel-Manzke syndrome is characterized by Pierre Robin sequence and a unique form of bilateral hyperphalangy causing a clinodactyly of the index finger. We describe the identification of homozygous and compound heterozygous mutations in TGDS in seven unrelated individuals with typical Catel-Manzke syndrome by exome sequencing. Six different TGDS mutations were detected: c.892A>G (p.Asn298Asp), c.270_271del (p.Lys91Asnfs*22), c.298G>T (p.A1a100Ser), c.294T>G (p.Phe98Leu), c.269A>G (p.G1u90Gly), and c.700T>C (p.Tyr234His), all predicted to be disease causing. By using haplotype reconstruction we showed that the mutation c.298G>T is probably a founder mutation. Due to the spectrum of the amino acid changes, we suggest that loss of function in TGDS is the underlying mechanism of Catel-Manzke syndrome. TGDS (dTDP-D-glucose 4,6-dehydrogenase) is a conserved protein belonging to the SDR family and probably plays a role in nucleotide sugar metabolism