A new CRISPR-based COVID diagnostic, seeking SNP-gene connections, and a portal for lipid droplet data.
Research Roundup: February 11, 2022
Welcome to the February 11, 2022 installment of Research Roundup, a recurring snapshot of recent studies published by scientists at the Broad Institute and their collaborators.
A pathogen-probing platform’s progress
A new CRISPR-based technology, mCARMEN, rapidly detects different COVID variants and other pathogens. To build it, a team led by Nicole Welch, Cameron Myhrvold (now at Princeton University), and institute member Pardis Sabeti in the Infectious Disease and Microbiome Program adapted their CARMEN platform, first developed with the Blainey lab, to be faster, more sensitive, and more easily implemented in clinical and surveillance labs. During the late-2021 Omicron surge, they used mCARMEN to estimate the variant’s prevalence in Massachusetts, which helped public health experts provide guidance to local hospitals. Described in Nature Medicine and a Broad news story, mCARMEN could potentially be used more widely during future outbreaks.
A new model for matching SNPs to genes
The majority of single nucleotide polymorphisms (SNPs) flagged in genome-wide association studies fall outside the coding genome, and connecting individual regulatory SNPs to the genes they influence is quite challenging. In the American Journal of Human Genetics, Dan Weiner, Steven Gazal, institute member Elise Robinson in the Stanley Center for Psychiatric Research, and Schmidt Fellow Luke O’Connor in the Program in Medical and Population Genetics propose an abstract mediation model (AMM) for estimating how much a given SNP's relationship with a trait is mediated by 1) the SNP's closest genes, and 2) a gene's known relevance to the trait of interest. Learn more in a tweetorial by Weiner.
Integrating lipid droplet datasets
Lipid droplets (LDs) are organelles bound by a single layer of phospholipids that store neutral lipids for energy metabolism and cell membrane homeostasis. Perturbations to LD biology are associated with atherosclerosis, cancer, neurodegeneration, and other diseases, but attempts to study LDs have been fragmented. The lab of associate members Robert Farese and Tobias Walther of the Metabolism Program, along with Broad colleagues, has created the Lipid Droplet Knowledge Portal, a platform that integrates transcriptomics, proteomics, and genomics data from fly, human, and mouse cells. LD-portal also connects to other databases such as the Common Metabolic Diseases Knowledge Portal. In Developmental Cell, the team describes several examples using LD-Portal to study LD biology.