High throughput single-cell detection of multiplex CRISPR-edited gene modifications

© The Author(s).
CRISPR-Cas9 gene editing has transformed our ability to rapidly interrogate the functional impact of somatic mutations in human cancers. Droplet-based technology enables the analysis of Cas9-introduced gene edits in thousands of single cells. Using this technology, we analyze Ba/F3 cells engineered to express single or multiplexed loss-of-function mutations recurrent in chronic lymphocytic leukemia. Our approach reliably quantifies mutational co-occurrences, zygosity status, and the occurrence of Cas9 edits at single-cell resolution.
C.J.W. acknowledges support from the NIH/National Cancer Institute (NIH/NCI) (R01 CA216273, U10 CA180861, P01 CA206978, and P01-CA081534) and is a scholar of the Leukemia and Lymphoma Society. E.t.H. is a Special Fellow of the Leukemia and Lymphoma Society and a Scholar of the American Society of Hematology. S.L. is supported by the NCI Research Specialist Award (R50CA251956-01). L.P. is supported by the National Human Genome Research Institute (NHGRI) Career Development Award (R00HG008399), Genomic Innovator Award (R35HG010717), and CEGS (RM1HG009490). MHS holds a Sara Borrell post-doctoral contract (CD19/00222) from the Instituto de Salud Carlos III (ISCIII) co-founded by Fondo Social Europeo (FSE) “El Fondo Social Europeo invierte en tu futuro”. M.G. was supported by a Marie-Curie International Outgoing Fellowship from the European Union (PIOF-2013-624924).