Table 1.
No‐call and discordant call rates in each sample type across all SNPs (n = 247) and by genotype.
| Blood | FFPE‐T | Comparison p‐valuei | FFPE‐LN | Comparison p‐valuei | FFPE‐T vs FFPE‐LN p‐value | |||
|---|---|---|---|---|---|---|---|---|
| No calls | Overalla | 0.5% (135/28158) | 4.3% (1221/28158) | <0.001 | 3.0% (843/28158) | <0.001 | <0.001 | |
| By genotypeb | Homozygous | NA | 1.8% (346/18900) | <0.001 | 2.5% (468/18900) | <0.001 | NA | |
| Heterozygous | NA | 9.5% (864/9123) | 4.0% (363/9123) | |||||
| Strict discordant callsc | Overalld | NA | 1.1% (306/26813) | NA | 0.3% (84/27192) | NA | <0.001 | |
| By genotypee | Homozygous | NA | 0.2% (33/18554) | <0.001 | 0.2% (32/18432) | <0.001 | NA | |
| Heterozygous | NA | 3.3% (273/8259) | 0.6% (52/8760) | |||||
| Direction of discordancef | Hom → Het | NA | 10.8% (33/306) | NA | 28.6% (24/84) | NA | NA | |
| Het → Hom | NA | 89.2% (273/306) | 61.9% (52/84) | |||||
| Hom → Hom | NA | 0% (0/306) | 9.5% (8/84) | |||||
| Possible discordant callsg | Overallh | NA | 5.9% (1651/28158) | NA | 3.7% (1050/28158) | NA | <0.001 | |
Abbreviations: Het = Heterozygous genotype call, Hom = Homozygous genotype call.
Overall no‐call rate calculated by: # no‐calls/28158 genotype calls (247 SNPs in 114 patients).
No‐call rate by genotype calculated by: # no‐calls/# calls of that genotype. Note this excludes 135 SNPs with no‐calls in blood.
Strict discordance defined as a genotype call was made in both blood and FFPE‐T (or FFPE‐LN) and the calls were different.
Overall strict discordant call rate calculated by: # genotype calls in FFPE‐T (or FFPE‐LN) that are different from genotype call in blood/# of genotype calls in FFPE‐T (or FFPE‐LN) and blood. Note that any sample with a no‐call in FFPE‐T (or FFPE‐LN) or blood excluded from calculation.
Strict discordance rate by genotype calculated by: # genotype calls in FFPE‐T (or FFPE‐LN) that are different from genotype call in blood/# of genotype calls in FFPE‐T (or FFPE‐LN) and blood of that genotype. Note that any sample with a no‐call in FFPE‐T (or FFPE‐LN) or blood excluded form calculation.
Type of discordance with the genotype call in blood first and the genotype call in the tissue of interest second. Percentage calculated as the # of discordant calls in that direction/the number of total discordant calls.
Possible discordance defined as either a strict discordant call was made or a genotype call was not made in blood or FFPE‐T (or FFPE‐LN).
Overall possible discordance calculated by: # of genotype calls in FFPE‐T (or FFPE‐LN) that are different from genotype calls in blood plus number of no‐calls in FFPE‐T (or FFPE‐LN) or blood/28158 genotype calls (247 SNPs in 114 patients).
P‐values compare FFPE‐T or FFPE‐LN vs. blood, FFPE‐T vs. FFPE‐LN, or homozygous vs. heterozygous within sample type, as appropriate.