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Single-cell multi-gene identification of somatic mutations and gene rearrangements in cancer.
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): zcad034Abstract
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