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Science Examines Combination of Gene Editing, Single Cell RNA Sequencing to Study Genetic Interactions

A combination of CRISPR gene editing and single-cell RNA sequencing is used to create a framework for studying genetic interactions (GIs) and their impact on cellular phenotypes in a study appearing in Science this week. The approach is based on a high-content phenotyping approach called single-cell RNA-seq pooled CRISPR screens, or Perturb-seq. The study's authors used Perturb-seq to manipulate a large number of gene pairs and then measure the resulting changes in cell state. "This ensemble of measurements described a high-dimensional surface called a GI manifold," they write. "By interpreting and modeling the GI manifold, we can gain several insights into how complex phenotypes emerge." Among their findings is an "unexpected synergy" between two genes in driving erythroid differentiation.

A personalized circulating tumor DNA (ctDNA) assay is able to detect signs of residual disease in women with breast cancer more effectively than existing methods, according to a study in Science Translational Medicine. Based on a technology called TARDIS — short for targeted digital sequencing — the assay can analyze multiple patient-specific mutations using input DNA equivalent to a single tube of blood. In 33 breast cancer patients, TARDIS was used to successfully analyze up to 115 mutations per patient in 80 plasma samples, detecting ctDNA in all patients prior to treatment and confirming lower ctDNA levels post-treatment. Notably, patients who responded the best to chemotherapy displayed a 96 percent decrease in ctDNA abundance, while patients with residual disease showed a 77 percent decrease, suggesting the platform could "enable individualized clinical management of patients with cancer treated with curative intent."