FOR 2841:  Beyond the Exome – Identifying, Analyzing, and Predicting the Disease Potential of Non-Coding DNA Variants

• Subject Area: Medicine ; Biology ; Computer Science, Systems and Electrical Engineering
• Term: from 2019 to 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 400728090

Although whole-exome sequencing of rare genetic diseases is almost routine, only a maximum of 50% patients can be molecularly elucidated. Theoretically, whole genome sequencing (WGS) could close this gap. However, clinicians and researchers face numerous difficulties in interpreting non-coding genomic variants, as there are no universal rules on the function of the regulatory genome. In a group of leading specialists and researchers from the fields of medicine, neuropathology, bioinformatics, single cell and organoid biology, we focus on a central problem in modern human genetics: how can variants affecting structural and regulatory regions in the non-coding genome, for which there are no generalizable rules, be confidently interpreted as a possible cause of genetic disease? Our hypothesis is that interpretation of disease-causing noncoding variants is possible if the major genomic regions involved in the development and maintenance of diseased tissue are known. We recognize that this will require an atlas of genomic regions for each disease group. Therefore, we focus on three exemplary disease groups: congenital myopathies and hypothyroidism and on somatic mutations resulting from acute kidney injury. We are taking a multi-pronged approach: improving the processing and bioinformatic analysis of raw WGS data, improving the understanding of the impact of 3D genome structure on gene regulation, collecting widely scattered gene regulation information in a central database, and exploring novel genomic regulatory mechanisms. Epigenetic data collected include histone modifications, chromatin states and contacts, high-resolution transcription factor binding sites, regulatory networks, and the effects of genome variants on chromatin contacts, structure, and function. To model early human development, we use iPSC-derived 2D and organoid cultures. This allows us to model organ development in culture and track epigenetic modifications during organ development at the single cell level from the beginning. Our bioinformaticians are using the research unit results to develop free software that will interpret the changes in the non-coding genome. We hope to use this software to bring WGS closer to routine clinical application. Beyond the Exome has access to well-characterized patients (cohorts) with developmental disorders of the thyroid and muscle, in whom a diagnosis has not yet been made despite WES and in whom we now want to elucidate the causes.

• DFG Programme: Research Units

Projects

• Clonal evolution of somatic mosaicism during acute-to-chronic kidney disease progression (Applicants Sanders, Ashley ;  Schmidt-Ott, Kai )
• Comprehensive repository of regulatory genomic features and their role in human disease (Applicants Leser, Ulf ;  Seelow, Dominik )
• Coordination Funds (Applicant Schülke-Gerstenfeld, Markus )
• Development of software for better assessment of non-coding variants on gene expression - translating the results from the research unit to clinical application (Applicant Seelow, Dominik )
• DNA recognition-element binding by GRHL/CP2-family and NKX2-1 transcription factors (Applicants Heinemann, Udo ;  Schmidt-Ott, Kai )
• Epigenomic mapping of myogenic regulation in human muscle development (Applicant Ohler, Uwe )
• Functional characterization of non-coding variants in disease-causing regions of benign choreoathetosis (CAHTP) and thyroid dysgenesis (CHTD) (Applicant Krude, Heiko )
• High resolution mapping of genomic elements relevant for muscle development as potential mutational hot-spots in patients with congenital myopathy and congenital muscle dystrophy (Applicants Gouti, Ph.D., Mina ;  Schülke-Gerstenfeld, Markus )
• Multi-sample structural variant calling with linked-read sequencing data (Applicant Kehr, Birte )
• Searching for the signature and causes of muscular dystrophies associated with nuclear envelope dysfunction using single-cell multiomics (Applicants Robson, Michael ;  Stenzel, Werner )
• The effects of non-coding duplications on gene regulation and disease pathology (Applicant Mundlos, Stefan )
• The role of dynamic gene expression in myogenic stem cells (Applicant Birchmeier, Carmen )

• Spokesperson: Professor Dr. Markus Schülke-Gerstenfeld