Applying this approach to five cryopreserved AML samples, we identify hundreds to thousands of cells containing tumor-specific mutations in each case, and use the results to distinguish AML cells (including normal-karyotype AML cells) from normal cells, identify expression signatures associated with ...
cells were cultured in DMEM containing 10% FBS and 1% of each penicillin and streptomycin at 37 °C in a 5% CO2 atmosphere for 2 days. On the day of single-cell capture, cells were trypsinized (0.05% Trypsin-EDTA solution),
Mutation somaticMice, pink-eyedRetinal pigmentThe retinal pigment epithelium (RPE) consists of a single layer of hexagonal cells, numbering about 10 5 in the 3-day mouse. Examination of the fixed and cleared RPE of mice homozygous for the unstable allele of pink-eye ( p um ), which shows...
study interpreted the normal-like methylation levels of the “off-target” tumors as a difference in cancer methylation patterns, our deconvolution results strongly suggest that it is due to the relatively low amount of cancer DNA circulating in the blood. The fraction of cancer cells in cfDNA (...
T. et al. Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics 28, 1811–1817 (2012). Article CAS PubMed Google Scholar Larson, D. E. et al. Somaticsniper: Identification of somatic point mutations in whole genome sequencing data. ...
AtaCNA accurately distinguished tumor and normal cells in various cancer types In the analysis of single-cell sequencing data from tumor samples, it is common to use CNAs to distinguish tumor cells. Therefore, we further validated the effectiveness of AtaCNA in this regard. We applied AtaCNA to...
Cells in carriers of germline BAP1 mutations have reduced levels of BAP1, about 50% than normal as these cells have only one normal BAP1 allele [14]. Human cells derived from carriers of germline BAP1 mutations showed reduced ability to repair DNA by homologous recombination and to execute ...
In a single case, CISH reveals very focal amplification, in <1% of tumor cells, which is not detected by NGS (red point). F: EGFR amplification in glioblastomas stratified by tumor cellularity. The proportion of EGFR-amplified samples per group is shown above the dot plot. Dotted horizontal...
Strelka2: fast and accurate calling of germline and somatic variants. Nat. Methods 15, 591–594 (2018). Article CAS PubMed Google Scholar Taylor-Weiner, A. et al. DeTiN: overcoming tumor-in-normal contamination. Nat. Methods 15, 531–534 (2018). Article CAS PubMed PubMed Central ...
1. A method for identifying somatic mutations in a human subject by analyzing a biological sample of the human subject, the biological sample including DNA fragments originating from normal cells and potentially from tumor cells or cells associated with cancer, the biological sample including cell-fre...