Table 2.
Summary of Genotyping Discrepancies Attributed to Research or Clinical Genotyping in eMERGE-PGx (from Subset of Sites with Available Resources for Repeat Analyses to Resolve Genotype Discrepancies)
| Site | Total samples, n | Research NGS |
Clinical genotyping |
||||||
|---|---|---|---|---|---|---|---|---|---|
| Preanalytical | Analytical | Postanalytical | Sample discrepancy rate attributed to research NGS | Preanalytical | Analytical | Postanalytical | Sample discrepancy rate attributed to clinical genotyping | ||
| Sample discrepancies | |||||||||
| A | 607 | 0 | 0 | 0 | 0 | 0 | 4∗ | 0 | 0.0066 |
| B | 442 | 3† | 0 | 0 | 0.0068 | 0 | 3‡ | 1§ | 0.0090 |
| C | 292 | 8¶ | 0 | 0 | 0.027 | 0 | 0 | 0 | 0 |
| D | 451 | 0 | 0 | 0 | 0 | 1‖ | 17∗∗ | 0 | 0.040 |
| Total | 1792 | 11 | 0 | 0 | 0.0061 | 1 | 24 | 1 | 0.015 |
| Site | Total variants, n | Research NGS |
Clinical genotyping |
||||||
|---|---|---|---|---|---|---|---|---|---|
| Preanalytical | Analytical | Postanalytical | Variant discrepancy rate attributed to research NGS | Preanalytical | Analytical | Postanalytical | Variant discrepancy rate attributed to clinical genotyping | ||
| Variant discrepancies | |||||||||
| A | 8498 | 0 | 0 | 0 | 0 | 0 | 4∗ | 0 | 0.00047 |
| B | 6188 | 5† | 0 | 0 | 0.00081 | 0 | 3‡ | 1§ | 0.00065 |
| C | 5256 | 33¶ | 0 | 0 | 0.0063 | 0 | 0 | 0 | 0 |
| D | 7216 | 0 | 0 | 0 | 0 | 1‖ | 17∗∗ | 0 | 0.0025 |
| Total | 27,158 | 38 | 0 | 0 | 0.0014 | 1 | 24 | 1 | 0.00096 |
NGS, next-generation sequencing.
In three independent DNA samples, rs9923231 was genotyped incorrectly because of allele dropout as a result of a rare 14-bp deletion variant underlying a commercial primer binding site; a software genotype calling error; and a low-quality call despite passing overall call rate quality control (confirmed on repeat testing). In one additional DNA sample, rs12248560 was genotyped incorrectly because of a low-quality call despite passing overall call rate quality control (confirmed on repeat testing).
Human error during sample aliquoting before DNA being sent for NGS genotyping resulted in three independent DNA samples being switched before research NGS. As a result, one variant (rs4244285) was incorrect in two samples and three variants (rs9923231, rs4149056, and rs1057910) were incorrect in one sample. One of these DNA sample switches was detected by the research NGS laboratory as an unexpected duplicate.
In three independent DNA samples, rs12248560 was genotyped incorrectly because of a nearby rare single-nucleotide variant underlying a commercial primer binding site.
For one DNA sample, correct genotyping results were translated incorrectly in the report because of human error.
Human error during sample aliquoting before DNA being sent for NGS genotyping resulted in eight independent DNA samples being switched before research NGS. As a result, two variants (rs12248560 and rs4244285) were incorrect in two samples, three variants were incorrect in two samples (rs4244285, rs1799853, and rs1057910 in one case, and rs7294, rs9934438, and rs9923231 in the other), four variants (rs12248560, rs4244285, rs9934438, and rs9923231) were incorrect in one sample, five variants (rs776746, rs12248560, rs4244285, rs4149056, and rs7294) were incorrect in one sample, six variants (rs12248560, rs4244285, rs4149056, rs7294, rs9934438, and rs9923231) were incorrect in one sample, and eight variants (rs776746, rs12248560, rs4244285, rs1799853, rs1057910, rs7294, rs9934438, and rs9923231) were incorrect in one sample. Two of these DNA sample switches were detected by the research NGS laboratory because of sex mismatch.
Human error resulted in one DNA sample being switched before clinical genotyping. As a result, one variant (rs7294) was incorrectly called in one sample by clinical genotyping.
In 15 independent DNA samples, rs12248560 was genotyped incorrectly because of allele dropout as a result of a single-nucleotide variant underlying a commercial primer binding site. In two additional independent DNA samples, rs4244285 was genotyped incorrectly because of allele dropout as a result of a single-nucleotide variant underlying a commercial primer binding site.