Review of study design, data QC and results
The Tumor Inflammation Signature (TIS) was predictive of response to Drug A, as were a number of lymphoid-related gene signatures. The sample size for Drug B was too small, and the results were consistent both with a model where TIS performs as it does in Drug A and with a model where TIS is not predictive of Drug B response.
A signature of B-cell abundance showed discordant patterns between the two drugs, predicting response to Drug A and non-response to Drug B. Signal in this experiment was variable, and we removed 4 samples due to low expression.
Signal QC
This plot shows the mean log2-transformed expression of the housekeeper genes in each sample. Housekeeper gene signal is a good metric of data quality. Samples with low housekeeper signal suffer from either low sample input or low reaction efficiency, and data quality is reduced in them. NanoString standard practice is to discard all samples in which the mean of the IO 360 housekeepers falls below 5 (32 raw counts). Ideally, all samples will have a housekeeper mean of at least 7 (128 raw counts).
Study design and sample annotation
The below table shows mean log2 housekeeping gene, TIS, and all sample annotations used in the analysis.| ID | Response | Days.PFS | Progression | Drug | TIS score | |
|---|---|---|---|---|---|---|
| 1 | SMP001 | PR/CR | 1258 | 0 | Drug A | 8.5482 |
| 2 | SMP002 | PD/SD | 23 | 1 | Drug A | 5.1614 |
| 3 | SMP003 | PD/SD | 413 | 1 | Drug A | 5.9334 |
| 4 | SMP004 | PD/SD | 222 | 1 | Drug A | 5.7286 |
| 5 | SMP005 | PD/SD | 15 | 1 | Drug A | 6.5733 |
| 6 | SMP006 | PD/SD | 35 | 1 | Drug A | 6.9021 |
| 7 | SMP007 | PD/SD | 60 | 1 | Drug A | 7.2739 |
| 8 | SMP008 | PD/SD | 47 | 1 | Drug A | 8.8182 |
| 9 | SMP009 | PR/CR | 1202 | 0 | Drug A | 6.7026 |
| 10 | SMP010 | PR/CR | 590 | 1 | Drug A | 6.2983 |
| 11 | SMP011 | PR/CR | 965 | 0 | Drug A | 7.9185 |
| 12 | SMP012 | PR/CR | 1271 | 0 | Drug A | 7.2317 |
| 13 | SMP013 | PD/SD | 42 | 1 | Drug A | 7.5895 |
| 14 | SMP014 | PD/SD | 222 | 1 | Drug A | 5.7285 |
| 15 | SMP015 | PD/SD | 80 | 1 | Drug A | 8.3822 |
| 16 | SMP016 | PD/SD | 222 | 1 | Drug A | 5.7548 |
| 17 | SMP017 | PR/CR | 527 | 0 | Drug A | 5.8336 |
| 18 | SMP018 | PR/CR | 1222 | 0 | Drug A | 7.8205 |
| 19 | SMP019 | PD/SD | 35 | 1 | Drug A | 8.0951 |
| 20 | SMP020 | PD/SD | 52 | 1 | Drug B | 6.1944 |
| 21 | SMP021 | PD/SD | 112 | 1 | Drug B | 6.1351 |
| 22 | SMP022 | PR/CR | 1091 | 0 | Drug B | 8.7378 |
| 23 | SMP023 | PD/SD | 62 | 1 | Drug B | 4.7003 |
| 24 | SMP024 | PD/SD | 80 | 1 | Drug B | 5.5719 |
| 25 | SMP025 | PR/CR | 1459 | 0 | Drug B | 7.2987 |
| 26 | SMP026 | PD/SD | 176 | 1 | Drug B | 5.9505 |
| 27 | SMP027 | PD/SD | 82 | 1 | Drug B | 6.3054 |
| 28 | SMP028 | PD/SD | 269 | 1 | Drug B | 5.9199 |
| 29 | SMP029 | PD/SD | 69 | 1 | Drug B | 8.0401 |
| 30 | SMP030 | PR/CR | 1076 | 0 | Drug B | 8.7311 |
| 31 | SMP031 | PD/SD | 15 | 1 | Drug B | 6.7552 |
| 32 | SMP032 | PD/SD | 25 | 1 | Drug B | 8.8213 |
| 33 | SMP033 | PR/CR | 1007 | 0 | Drug B | 7.1255 |
| 34 | SMP034 | PD/SD | 211 | 0 | Drug B | 6.7549 |
| 35 | SMP035 | PR/CR | 1281 | 0 | Drug B | 8.4908 |
| 36 | SMP036 | PD/SD | 126 | 1 | Drug B | 9.1774 |
| 37 | SMP037 | PD/SD | 96 | 1 | Drug B | 7.2592 |
| 38 | SMP038 | PD/SD | 475 | 1 | Drug B | 5.1256 |
| 39 | SMP039 | PD/SD | 71 | 1 | Drug B | 6.6376 |
| 40 | SMP040 | PD/SD | 49 | 1 | Drug B | 8.8831 |
| 41 | SMP041 | PD/SD | 503 | 1 | Drug B | 6.5691 |
| 42 | SMP042 | PD/SD | 69 | 1 | Drug B | 7.0526 |
| 43 | SMP043 | PD/SD | 197 | 1 | Drug B | 7.7338 |
| 44 | SMP044 | PD/SD | 72 | 1 | Drug B | 6.6677 |
| 45 | SMP045 | PR/CR | 253 | 0 | Drug B | 6.7959 |
| 46 | SMP046 | PD/SD | 100 | 1 | Drug B | 5.9169 |
| 47 | SMP047 | PD/SD | 205 | 1 | Drug B | 6.0152 |
| 48 | SMP048 | PR/CR | 1205 | 0 | Drug B | 7.2838 |
| 49 | SMP049 | PR/CR | 723 | 1 | Drug B | 5.3339 |
| 50 | SMP050 | PD/SD | 205 | 1 | Drug B | 6.8933 |
| 51 | SMP051 | PR/CR | 279 | 0 | Drug B | 9.3315 |
| 52 | SMP052 | PR/CR | 721 | 0 | Drug B | 6.7379 |
| 53 | SMP053 | PR/CR | 712 | 0 | Drug B | 8.2314 |