Single-cell multi-gene identification of somatic mutations and gene rearrangements in canceropen access
- Authors
- Grimes, Susan M; Kim, Heon Seok; Roy, Sharmili; Sathe, Anuja; Ayala, Carlos I; Bai, Xiangqi; Almeda-Notestine, Alison F; Haebe, Sarah; Shree, Tanaya; Levy, Ronald; Lau, Billy T; Ji, Hanlee P
- Issue Date
- Jul-2023
- Publisher
- Oxford University Press
- Citation
- NAR Cancer, v.5, no.3, pp.1 - 17
- Indexed
- SCIE
SCOPUS
- Journal Title
- NAR Cancer
- Volume
- 5
- Number
- 3
- Start Page
- 1
- End Page
- 17
- URI
- https://scholarworks.bwise.kr/hanyang/handle/2021.sw.hanyang/191764
- DOI
- 10.1093/narcan/zcad034
- ISSN
- 2632-8674
- 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.
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