Human Genetic Variation and Disease

In this renewal, we will continue our studies of the causes and disease consequences of human genetic variation. We have generated whole-genome sequence (WGS) data from the three-generation Utah CEPH pedigrees to longitudinally characterize rates and patterns of de novo mutations (DNMs). We showed significant differences in the rates of accumulation of mutations among families, and we demonstrated that 10% of apparent DNMs are actually postzygotic events that result in mosaicism. We also showed that a higher rate of age-adjusted germline DNM transmission is significantly associated with a shorter lifespan and earlier menopause. These results imply that one’s germline DNM rate, which increases with age, is associated with the somatic mutation rate. In the next funding period, we will test this hypothesis directly using blood-derived DNA samples collected at three different time points in the same CEPH pedigree members over a 35-year time period. To our knowledge, this is the first long-term longitudinal study of germline and somatic mutation rates in human pedigrees. We also hypothesize that DNA repair mechanisms influence variation in both germline and somatic mutation rates. We will test this hypothesis using whole-genome sequence data (supported by separate funding) and RNA-seq data from freshly collected whole blood samples. We predict that lower expression of critical DNA repair genes will result in higher germline and somatic mutation rates. To increase our power to detect patterns and disease associations, we will (under separate funding) expand the CEPH pedigree collection to include more than 700 members of the fourth generation, who are now adults. We will also resample generations 2 and 3 for a third time. We will undertake WGS and RNA-seq in these study participants, creating a unique, publicly available repository of genetic information spanning four generations. More than 180 phenotypic measurements were made for generations 2 and 3 of the CEPH pedigrees 20 years ago, and the same measurements will be made for generation 4. These resources will allow us to explore the effects of genetic variation, including mutation rates and DNA repair, on a broad assortment of phenotypes across several generations. In addition, we will continue our work to develop new and improved methods for genome sequence analysis, including the detection of mobile element insertions. We will analyze WGS and RNA-seq data from members of large Utah disease pedigrees obtained from the Utah Population Database, focusing on amyotrophic lateral sclerosis and juvenile idiopathic arthritis. These projects involve analysis of WGS and RNA-seq data as well as functional analysis in in vitro and in vivo systems.