The Dennis lab has published its first lead-authored paper “Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing” in a special issue of Genes: A Tale of Genes and Genomes, led by IGG PhD students Daniela Soto and Colin Shew with support from lab members, including research specialists Mira Mastoras and Gulhan Kaya, the UC Davis Genome Center core (Ruta Sahasrabudhe), as well as collaborator Aida Andrés and her group.

Some highlights:

Identified deletions and inversions (SVs) in two chimpanzees vs. a human reference using nanopore and optical mapping, including 88 novel deletions and 36 novel inversions.
Coupled with RNA-seq and Hi-C data from LCLs and IPSCs, we found SVs to be enriched for differentially-expressed genes between human and chimpanzee and depleted for TAD boundaries, recapitulating work from others.
Generated TAD maps directly comparing human and chimpanzee that show how inversions and deletion can perturb the chromatin landscape.
Highlighted genes found impacted uniquely in chimpanzees, that may play a role in species-specific traits (including some exhibiting signature of positive/balancing selection).
This represents the first nanopore sequencing of a chimpanzee (a western female) and, importantly, all our data is available for download (Illumina, ONT, bionano, and Hi-C) on our github page here.