Concurrent Workshop (Genomics): GERG (Genome Editing Research Group/GBIRG (Genome Bioinformatics Research Group)
Reproducibility of indel formation rates by comparing guideRNA format and delivery method
Multiple configurations of guideRNA and Cas9 components can be used for editing cells. A few options include: a plasmid expressing both the guideRNA and Cas9, Cas9 protein combined with a synthetic single guideRNA, and Cas9 combined with a synthetic 2-part guideRNA. In addition, delivering the components to cells can be done using lipofection or nucleofection transfection methods. In the GERG 2017 survey (https://abrf.org/sites/default/files/gerg_survey_poster_2018_final_0.pdf), plasmid format and lipofection delivery were favored among cell culture users. Meanwhile, RNP format for the guideRNA and Cas9 protein is gaining in popularity in combination with nucleofection delivery. The GERG 2018 study compared the cutting efficiency at 3 different guideRNA targets based on the guideRNA format and delivery method across multiple labs. Determining which method or format is the most reproducible will be beneficial. Core facilities or research labs getting started with genome editing could use these results as a benchmark for optimizing their own protocols.
Distribution of microbial communities and antimicrobial resistances in urban environments and on the ISS space station
The majority of the world’s population lives in cities, yet our understanding of the dynamics and distribution of bacteria, viruses, and antimicrobial resistance (AMR) genes in urban built environments is limited. Cities and urban transport hubs like metro stations and airports represent the sites of highest human population density, and are thus hotspot areas for microbial and genetic exchange in both developing and developed countries. Moreover, most inhabitants, visitors and passenger carry a mobile phone, which serves as a “molecular echo” of the travel history of a person as well as a representation of his or her personal microbiome.
Through leveraging next-generation sequencing (NGS) and metagenome sequencing methods, combined with rapid computational analysis, we can reveal the microbial and genetic profiles, AMR gene content, localization, and movement patterns ‘imprinted’ on phones and city surfaces, as readily as for clinical samples.
International Consortium for Metagenomics of Subways and Urban Biomes (MetaSUB) at Weill Cornell Medicine, which is funded by the NIH, WorldQuant, and the Bill and Melinda Gates Foundation. We are currently analyzing >5.000 whole-genome shotgun metagenomes using samples collected in the subways (15000 samples total of more than 85 cities in 21 different countries. In parallel we analyzed for interrogating microbiomes obtained from > 2000 mobile phone surfaces, which we showcased during several international conferences. To our knowledge this is the first study investigating a comprehensive and worldwide view of urban microbiomes and AMR exchange.
To complement our knowledge, we are comparing the generated metagenomes with data collected by the Extreme Microbiome Project and microbial isolates collected at the ISS by NASA during the last 11 years. Furthermore, to evaluate our findings and improve the accuracy of microbiome analyses, we developed novel protocols for metagenomic linked-DNA genomic sequencing (using 10X Genomics Chromium) and long-read sequencing (using Oxford Nanopore MinION and PromethION sequencers).
Genetic Analysis Tools for Genome Editing Workflows
Thermo Fisher Scientific is your trusted partner for genome analysis solutions. In this talk, we will describe how our solutions are used in genome editing experiments, including why knowing genome editing efficiency is important, the different mechanisms used to analyze editing efficiency, and finally the advantages of the different technologies as applied to particular problems.