Complete human parent-of-origin genome: functional signatures and developmental determinants of disease. - SUMMARY There are over 10 million children in the US suffering from rare disease, most of these diseases are genetic and require DNA sequencing for diagnosis, however even with contemporary clinical sequencing and knowledge of thousands of diseases most patients remain undiagnosed. One area of understudied rare disease is imprinting diseases with only dozen diseases known to date, where developmentally the parental copies (maternal and paternal) of genes are regulated differentially and the DNA variants can be harmful only if inherited from either mother or father. This regulatory difference can be read by sequencing DNA CpG-methylation. The Genomic Medicine Center (GMC) at Children’s Mercy Kansas City (CMKC) has spearheaded systematic generation of full genomes by long-read 5-base sequencing (5mC-HiFi-GS) that collects CpG-methylation data in parallel with all genetic variation and applied it to thousands of rare disease families, including families suffering from unusual pregnancy losses building a comprehensive resource of long-read, parentally resolved genomes across different human cell types and developmental stages. Using this 5mC-HiFi-GS resource we have found hundreds of genes and thousands CpG dinucleotides not previously known to be imprinted to show unequivocal evidence of parent-of-origin (PofO). These observations are harnessed here to characterize new diseases and developmental processes governed by parental differences in gene regulation. Specifically, we will develop a comprehensive and enhanced map of human imprinted genes or “imprintome” in the 5mC-HiFi-GS resources, which includes optimized technology, scale and sample procurement for sensitively and specifically detecting PofO dependent DNA in human genome. The PofO regions in genome are then characterized by single nuclei epigenome analyses and long-read RNA sequencing to link each novel imprinted sequence to its target gene. Finally, in three rare disease cohorts we will look for new variants and diseases caused by perturbation in PofO regulated genes and DNA. In parallel, we will study the overall developmental influences of these gene regions beyond specific rare diseases using common variation in growth (e.g. height) using our patient cohorts and then validate in population samples (UK Biobank). Through the extensive new information on human genome regulation differentially between maternal and paternal copies combined with detailed family-based cohorts we will uncover new determinants of development and disease in this understudied layer of human genome variation.
