Notice: Users may be experiencing issues with displaying some pages on stanfordhealthcare.org. We are working closely with our technical teams to resolve the issue as quickly as possible. Thank you for your patience.
 

Learn about the flu shot, COVID-19 vaccine, and our masking policy »

Stanford Health Care

Single-cell multi-gene identification of somatic mutations and gene rearrangements in cancer. NAR cancer Grimes, S. M., Kim, H. S., Roy, S., Sathe, A., Ayala, C. I., Bai, X., Almeda-Notestine, A. F., Haebe, S., Shree, T., Levy, R., Lau, B. T., Ji, H. P. 2023; 5 (3): zcad034

Abstract

In this proof-of-concept study, we developed a single-cell method that provides genotypes of somatic alterations found in coding regions of messenger RNAs and integrates these transcript-based variants with their matching cell transcriptomes. We used nanopore adaptive sampling on single-cell complementary DNA libraries to validate coding variants in target gene transcripts, and short-read sequencing to characterize cell types harboring the mutations. CRISPR edits for 16 targets were identified using a cancer cell line, and known variants in the cell line were validated using a 352-gene panel. Variants in primary cancer samples were validated using target gene panels ranging from 161 to 529 genes. A gene rearrangement was also identified in one patient, with the rearrangement occurring in two distinct tumor sites.

View details for DOI 10.1093/narcan/zcad034

View details for PubMedID 37435532

View details for PubMedCentralID PMC10331933