During our workshop at this year’s AGBT conference, scientist Chris Mason from Weill Cornell Medicine intrigued the audience with a look at several ongoing projects in his lab. Mason is best known in the genomics field for PathoMap, a study of the microbial inhabitants of New York City, and for the NASA twins study, which uses an integrative ’omics approach to analyze the effects of space travel by comparing twin astronauts — one in space and one here on Earth. He has also done considerable RNA methods work and was the first to coin the word “epitranscriptome.” His team has been using QIAGEN tools, and he shared his experiences with our solutions.
One of Mason’s major efforts is MetaSUB, or PathoMap on steroids. For MetaSUB, scientists are analyzing microbial communities in 45 cities around the world, using subways and other urban infrastructure to get a better understanding of how microbes live, move, and pass among humans. Among other things, these studies are shedding light on important traits such as drug resistance; non-resistant and antibiotic-resistant bacteria could be found living in the same subway station in New York. As part of this project, the lab has been using CLC Genomics Workbench and CLC Microbial Genomics Module to analyze 16S rRNA data. Thanks to our recent partnership with CosmosID, our solution will soon have whole metagenome taxonomic analysis capabilities as well. Mason’s team is also working on the Extreme Microbiome Project to conduct similar studies in unusual locations around the world.
A similar approach, including CLC Genomics Workbench, is being used to study previously collected patient samples that were never successfully cultured. Mason said 20 to 30 percent of patients with infectious disease fall into this category — waiting for weeks for culturing of their samples, only to get inconclusive results. This project will sequence 250 such samples and use metagenomics to determine the microbial content.
In separate work, the Mason lab is using RNA-seq to look at differentially expressed genes in clinical samples. One project used the QIAseq Targeted RNA Panels to look at samples from leukemia patients taken at the time of diagnosis and again at relapse. The goal was to find genes consistently dysregulated at relapse — something that previous exome studies had failed to detect. The protocol worked well even with samples as small as 10 nanograms, and the all-in cost of about 50 cents per target gave a good option for quickly and affordably measuring gene expression. This study led to the validation of 104 genes that appear to be a signature of relapse in these patients.
One of the essential features of the QIAseq panels is the ability to add unique molecular identifiers, or barcodes, to each molecule prior to library prep, according to Mason. This step helps scientists detect PCR artifacts and correct ratios later in the workflow, making the process more robust and reliable.
Thanks to Chris Mason for an excellent talk about some of the fascinating research going on in his lab!
Watch the presentation on Targeted RNA sequencing, Urban Metagenomics, and Astronaut Genomics: