Grad student Daniela Soto gives webinar on chimpanzee SV project

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Graduate student Daniela Soto recently gave a webinar via Oxford Nanopore Technologies on our recent publication of chimpanzee structural variants (SVs; a joint co-authored project with graduate student Colin Shew). If you are interested in learning how to apply ONT and optical mapping reads to discover novel SVs and didn’t get a chance to check it out live, the recording is available here.

Farewell to team members KaeChandra, Aditya, and Elizabeth and updates

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The Dennis lab wants to congratulate junior specialist KaeChandra Weyenberg as she departs to pursue her master’s degree in Public Health from East Tennessee University.

We are also happy to send off graduating undergrads Aditya Sriram and Elizabeth Roberts. Aditya is headed to the University of Washington to pursue a master’s degree in Epidemiology and Elizabeth will pursue research at the Broad Institute in the Lander lab as she prepares to apply to grad school in the future.

We are also celebrating the news of several former Dennis lab undergrads:

  • Maram Bader has accepted an offer of admission to San Jose State University’s master’s in Microbiology and Molecular Biology program.

  • Dhriti Jagannathan plans to join the Genetic Counseling master’s program at the University of Minnesota.

  • Juliann Wang will start medical school at the University of Alabama at Birmingham School of Medicine.

2020 TAGC virtual conference

Third year IGG grad student José Uribe Salazar and PI Megan represented the Dennis lab at The Allied Genetic Conference (TAGC) this past week, showcasing two zebrafish projects ongoing in the group. José presented in the Zebrafish Neurogenetics session on a human-duplicated SRGAP2 zebrafish model and Megan presented in the Zebrafish Technologies session on a parallel-phenotyping platform to screen for multiple neurodevelopmental features in larvae. Talks were recorded and available (with conference registration) until mid-May via the TAGC website.

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Structural variant discovery in chimpanzees using long-read sequencing

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.

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UC Davis Human Genomics symposium

Congratulations to junior research specialist KaeChandra Weyenberg for winning a poster award at the UC Davis Human Genomics symposium on her work using zebrafish to characterize genes important in neurodevelopmental disorders (her first ever presented research poster!).

Also, the Dennis lab was represented by excellent presentations from additional lab members, including grad student Daniela Soto and undergrad Matangi Kumar. It was a fun, information-packed day full of impressive human genomic research ongoing at UC Davis!

Alex on Capitol Hill


Alex took part in the 12th annual Society for Neuroscience Capitol Hill Day on March 8th as part of a group of scientists who met with senators and representatives to advocate for a more consistent and robust increase in funding for the NIH, NSF and the BRAIN Initiative. Her visit included meeting with 3 senators, including Kamala Harris, and 5 representatives, including Nancy Pelosi.

SfN California trainees with Jackie Speier, representative for California's 14th district. Alex is pictured third from the right.

SfN California trainees with Jackie Speier, representative for California's 14th district. Alex is pictured third from the right.

Dennis lab members at ASBMB special symposium

Paulina and Colin recently attended the meeting “Evolution and Core Processes in Gene Expression”, a special symposium from the American Society for Biochemistry and Molecular Biology (ASBMB), held at Stowers Institute for Medical Research in Kansas City, MO.

Paulina presented the poster “The birth of regulatory elements within human-specific genomic duplicated regions”, which had good reception and comments. Both really enjoyed their time at Stowers, the talks were very useful and interesting. Overall, it was a great opportunity for knowing others working on gene expression and evolution.

Detailed information about the meeting program can be found here:

http://www.asbmb.org/SpecialSymposia/2017/geneexpression/program/

Stowers Institute for Medical Research

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Paulina named semifinalist

Paulina

Congratulations to Paulina Carmona-Mora for being named a one of 61 semifinalists from ~500 applicants for the 2017 Charles J. Epstein Trainee Awards for Excellence in Human Genetics Research for the 67th Annual Meeting of the American Society of Human Genetics. The upcoming meeting will be held in Orlando, FL, October 17-21. Wishing you the best of luck, Paulina!

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