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

Autor:	Grimes SM; Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA., Kim HS; Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA., Roy S; Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA., Sathe A; Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA., Ayala CI; Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA., Bai X; Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA., Almeda-Notestine AF; Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA., Haebe S; Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA., Shree T; Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA., Levy R; Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA., Lau BT; Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA., Ji HP; Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.; Department of Engineering, Stanford University, Stanford, CA 94305, USA.
Jazyk:	angličtina
Zdroj:	NAR cancer [NAR Cancer] 2023 Jul 10; Vol. 5 (3), pp. zcad034. Date of Electronic Publication: 2023 Jul 10 (Print Publication: 2023).
DOI:	10.1093/narcan/zcad034
Abstrakt:	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. (© The Author(s) 2023. Published by Oxford University Press on behalf of NAR Cancer.)
Databáze:	MEDLINE
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