Table 1 Overview of mutation discovery and detection in eWGS and scRNA-seq data
From: A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing
Sample | 508084 | 548327 | 721214 | 782328 | 809653 | Mean [SD] |
|---|---|---|---|---|---|---|
No. cells | 14,964 | 11,620 | 20,474 | 21,731 | 21,038 | 17,965 [3979] |
Reads/cell | 192,427 | 346,965 | 176,035 | 214,284 | 189,751 | 223,892 [62,745] |
Reads mapped confidently to genome (%) | 84.9 | 87.2 | 92.2 | 79.8 | 90 | 87 [4.29] |
Reads mapped confidently to transcriptome (%) | 64.2 | 63.7 | 73 | 61.9 | 68.8 | 66 [4.04] |
Median genes detected per cell | 2405 | 1383 | 2260 | 1376 | 1829 | 1851 [428] |
Total genes detected | 22,645 | 22,503 | 23,376 | 25,389 | 23,102 | 23,403 [1041] |
WGS variants | 19 | 13 | 41 | 31 | 28 | 26.4 |
Expressed WGS variants (bulk) | 10 | 5 | 18 | 7 | 8 | 9.6 |
scRNA-seq variants | 8 | 7 | 17 | 12 | 8 | 10.4 |
Percentage expressed WGS variants discovered in scRNA-seq | 80% | 140% | 94% | 170% | 100% | 117% |
Total mutant cells | 669 | 6042 | 8200 | 3354 | 386 | 3732 |
Mutant cells per variant | 13–453 | 1–3012 | 1–3944 | 1–2619 | 1–207 | 3.4–2047 |
Mutant cells per variant (median) | 32 | 48 | 30 | 111 | 21.5 | 48.5 |
Key WGS variants (no. cells with scRNA-seq coverage at variant position) | IKBKBV616M (150) FLT3-ITD (707) NUP98-NDS1(1) | IDH1R132H (118) NPM1W288fs (5591) SRSF2P95H (2349) | DNMT3A R882H (409) FLT3-ITD (479) FLT3F612L (306) NPM1W288fs (11,672) GATA2R361C (1629) | NRASG12S (949) NRASG12D (951) U2AF1S34F (4509) | NRASG12D (1412) TP53E286G (239) CEBPA R142fs (84) | N/A |
Additional variants with expression signature (number of cells with coverage) | RNF10 (103) | NAGLU E634K (216) | N/A |
